tests/testthat/_snaps/options_helper.md
In cancerit/RCRISPR: R Functions for CRISPR-Related Analyses
shared output options
Code
shared_output_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] "-r"
Slot "long_flag":
[1] "--rdata"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "rdata"
Slot "default":
NULL
Slot "help":
[1] "output file for .Rdata"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
[[2]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] "-d"
Slot "long_flag":
[1] "--outdir"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "outdir"
Slot "default":
NULL
Slot "help":
[1] "output directory"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
[[3]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] "-p"
Slot "long_flag":
[1] "--prefix"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "prefix"
Slot "default":
NULL
Slot "help":
[1] "output file prefix"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
[[4]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] "-s"
Slot "long_flag":
[1] "--suffix"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "suffix"
Slot "default":
NULL
Slot "help":
[1] "output file suffix"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
basic outfile options
Code
basic_outfile_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] "-o"
Slot "long_flag":
[1] "--outfile"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "outfile"
Slot "default":
NULL
Slot "help":
[1] "output file"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
count path options
Code
count_path_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] "-c"
Slot "long_flag":
[1] "--counts"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "counts"
Slot "default":
NULL
Slot "help":
[1] "path to directory of counts or a count matrix"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
count type options
Code
count_type_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--counts_type"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "counts_type"
Slot "default":
[1] "single"
Slot "help":
[1] "count type (must be either 'single' or 'matrix') [Default: single]"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
count format options
Code
count_format_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--no_counts_header"
Slot "action":
[1] "store_true"
Slot "type":
[1] "logical"
Slot "dest":
[1] "no_counts_header"
Slot "default":
[1] FALSE
Slot "help":
[1] "count file has no header"
Slot "metavar":
character(0)
Slot "callback":
NULL
Slot "callback_args":
list()
[[2]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--counts_delim"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "counts_delim"
Slot "default":
[1] "\t"
Slot "help":
[1] "count file delimiter [Default: \\t]"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
count column index options
Code
count_column_index_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--count_id_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "integer"
Slot "dest":
[1] "count_id_column_index"
Slot "default":
[1] 1
Slot "help":
[1] "index of id column in counts [Default: 1]"
Slot "metavar":
[1] "integer"
Slot "callback":
NULL
Slot "callback_args":
list()
[[2]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--count_gene_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "integer"
Slot "dest":
[1] "count_gene_column_index"
Slot "default":
[1] 2
Slot "help":
[1] "index of gene column in counts [Default: 2]"
Slot "metavar":
[1] "integer"
Slot "callback":
NULL
Slot "callback_args":
list()
[[3]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--count_count_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "count_count_column_index"
Slot "default":
[1] "3"
Slot "help":
[1] "index of columns containing counts (e.g. 3 or 3,4,5 or 3-5 or 3-5,6-8) [Default: 3]"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
library annotation options
Code
library_annotation_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] "-l"
Slot "long_flag":
[1] "--library"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "library"
Slot "default":
NULL
Slot "help":
[1] "library file containing guide identifiers and annotations"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
library annotation format options
Code
library_annotation_format_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--no_library_header"
Slot "action":
[1] "store_true"
Slot "type":
[1] "logical"
Slot "dest":
[1] "no_library_header"
Slot "default":
[1] FALSE
Slot "help":
[1] "library has no header"
Slot "metavar":
character(0)
Slot "callback":
NULL
Slot "callback_args":
list()
[[2]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--library_delim"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "library_delim"
Slot "default":
[1] "\t"
Slot "help":
[1] "library delimiter [Default: \\t]"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
library annotation column index options
Code
library_annotation_column_index_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--library_id_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "integer"
Slot "dest":
[1] "library_id_column_index"
Slot "default":
[1] 1
Slot "help":
[1] "index of column containing guide id in library annotations [Default: 1]"
Slot "metavar":
[1] "integer"
Slot "callback":
NULL
Slot "callback_args":
list()
[[2]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--library_gene_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "integer"
Slot "dest":
[1] "library_gene_column_index"
Slot "default":
[1] 2
Slot "help":
[1] "index of column containing gene name(s) in library annotations"
Slot "metavar":
[1] "integer"
Slot "callback":
NULL
Slot "callback_args":
list()
library annotation genomic column index options
Code
library_annotation_genomic_column_index_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--library_chr_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "library_chr_column_index"
Slot "default":
NULL
Slot "help":
[1] "index of column containing chromosome name in library annotations"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
[[2]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--library_start_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "library_start_column_index"
Slot "default":
NULL
Slot "help":
[1] "index of column containing chromosome start position in library annotations"
Slot "metavar":
[1] "integer"
Slot "callback":
NULL
Slot "callback_args":
list()
[[3]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--library_end_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "library_end_column_index"
Slot "default":
NULL
Slot "help":
[1] "index of column containing chromosome end position in library annotations"
Slot "metavar":
[1] "integer"
Slot "callback":
NULL
Slot "callback_args":
list()
sample metadata options
Code
sample_metadata_options()
sample metadata format options
Code
sample_metadata_format_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--no_info_header"
Slot "action":
[1] "store_true"
Slot "type":
[1] "logical"
Slot "dest":
[1] "no_info_header"
Slot "default":
[1] FALSE
Slot "help":
[1] "sample metadata has no header"
Slot "metavar":
character(0)
Slot "callback":
NULL
Slot "callback_args":
list()
[[2]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--info_delim"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "info_delim"
Slot "default":
[1] "\t"
Slot "help":
[1] "sample metadata delimiter [Default: \\t]"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
sample metadata sample filename options
Code
sample_metadata_sample_filename_column_index_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--info_filename_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "integer"
Slot "dest":
[1] "info_filename_column_index"
Slot "default":
[1] 1
Slot "help":
[1] "index of column containing sample count filename in sample mapping [Default: 1]"
Slot "metavar":
[1] "integer"
Slot "callback":
NULL
Slot "callback_args":
list()
sample metadata sample label options
Code
sample_metadata_sample_label_column_index_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--info_label_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "integer"
Slot "dest":
[1] "info_label_column_index"
Slot "default":
[1] 2
Slot "help":
[1] "index of column containing sample labels in sample mapping [Default: 2]"
Slot "metavar":
[1] "integer"
Slot "callback":
NULL
Slot "callback_args":
list()
sample metadata sample type options
Code
sample_metadata_sample_type_column_index_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--info_plasmid_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "integer"
Slot "dest":
[1] "info_plasmid_column_index"
Slot "default":
NULL
Slot "help":
[1] "index of column indicating whether sample type is plasmid in sample mapping"
Slot "metavar":
[1] "integer"
Slot "callback":
NULL
Slot "callback_args":
list()
[[2]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--info_control_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "integer"
Slot "dest":
[1] "info_control_column_index"
Slot "default":
NULL
Slot "help":
[1] "index of column indicating whether sample type is control in sample mapping"
Slot "metavar":
[1] "integer"
Slot "callback":
NULL
Slot "callback_args":
list()
[[3]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--info_treatment_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "integer"
Slot "dest":
[1] "info_treatment_column_index"
Slot "default":
NULL
Slot "help":
[1] "index of column indicating whether sample type is treatment in sample mapping"
Slot "metavar":
[1] "integer"
Slot "callback":
NULL
Slot "callback_args":
list()
sample metadata sample group options
Code
sample_metadata_sample_group_column_index_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--info_group_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "info_group_column_index"
Slot "default":
NULL
Slot "help":
[1] "index of column containing sample group name in sample mapping"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
sample metadata sample read count options
Code
sample_metadata_sample_read_count_column_index_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--info_reads_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "info_reads_column_index"
Slot "default":
NULL
Slot "help":
[1] "index of column containing sample read counts in sample mapping"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
duplicate guide options
Code
duplicate_guide_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--duplicate_guides_outfile"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "duplicate_guides_outfile"
Slot "default":
NULL
Slot "help":
[1] "output file for duplicate guides"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
remove guide options
Code
remove_guide_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--guides_to_remove"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "guides_to_remove"
Slot "default":
NULL
Slot "help":
[1] "file of guides to remove"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
MAGeCK RRA summary options
Code
mageck_rra_summary_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--gene_summary"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "gene_summary"
Slot "default":
NULL
Slot "help":
[1] "MAGeCK RRA gene summary"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
[[2]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--sgrna_summary"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "sgrna_summary"
Slot "default":
NULL
Slot "help":
[1] "MAGeCK RRA gene summary"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
[[3]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--n_genes"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "n_genes"
Slot "default":
[1] "10"
Slot "help":
[1] "number of genes to label in plots (in each direction)"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
[[4]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] "-f"
Slot "long_flag":
[1] "--fdr"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "fdr"
Slot "default":
[1] "0.05"
Slot "help":
[1] "maximum FDR value"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
BAGEL normalisation options
Code
bagel_normalisation_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--pseudocount"
Slot "action":
[1] "store"
Slot "type":
[1] "double"
Slot "dest":
[1] "pseudocount"
Slot "default":
[1] 5
Slot "help":
[1] "pseudocount to add to sample counts"
Slot "metavar":
[1] "numeric"
Slot "callback":
NULL
Slot "callback_args":
list()
[[2]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--scaling_factor"
Slot "action":
[1] "store"
Slot "type":
[1] "double"
Slot "dest":
[1] "scaling_factor"
Slot "default":
[1] 1e+07
Slot "help":
[1] "scaling factor for normalised counts"
Slot "metavar":
[1] "numeric"
Slot "callback":
NULL
Slot "callback_args":
list()
Calculate LFC options
Code
calculate_lfc_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--sgrna_outfile"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "sgrna_outfile"
Slot "default":
NULL
Slot "help":
[1] "output file for sgRNA-level fold change matrix"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
[[2]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--gene_outfile"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "gene_outfile"
Slot "default":
NULL
Slot "help":
[1] "output file for gene-level fold change matrix"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
[[3]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--count_matrix_outfile"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "count_matrix_outfile"
Slot "default":
NULL
Slot "help":
[1] "output file for count matrix"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
[[4]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--control_indices"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "control_indices"
Slot "default":
NULL
Slot "help":
[1] "pseudocount to add to sample counts"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
[[5]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--treatment_indices"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "treatment_indices"
Slot "default":
NULL
Slot "help":
[1] "scaling factor for normalised counts"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
[[6]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--pseudocount"
Slot "action":
[1] "store"
Slot "type":
[1] "double"
Slot "dest":
[1] "pseudocount"
Slot "default":
[1] 0.5
Slot "help":
[1] "pseudocount to add to sample counts"
Slot "metavar":
[1] "numeric"
Slot "callback":
NULL
Slot "callback_args":
list()
Remove guides with no coordinates options
Code
remove_no_coordinate_guide_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--excluded_guides_outfile"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "excluded_guides_outfile"
Slot "default":
NULL
Slot "help":
[1] "file of guides that were remove"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
Filter counts and library by index options
Code
filter_by_index_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--filter_indices"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "filter_indices"
Slot "default":
NULL
Slot "help":
[1] "column indices to use for filtering"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
[[2]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--filter_method"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "filter_method"
Slot "default":
NULL
Slot "help":
[1] "filter method ( all, any, mean or median ) [Default: all]"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
[[3]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--min_reads"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "min_reads"
Slot "default":
[1] "30"
Slot "help":
[1] "minimum number of reads for filtering [Default: 30]"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
CRISPRcleanR output options
Code
crisprcleanr_output_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--count_matrix_outfile"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "count_matrix_outfile"
Slot "default":
NULL
Slot "help":
[1] "output file for processed count matrix"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
[[2]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--lfc_matrix_outfile"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "lfc_matrix_outfile"
Slot "default":
NULL
Slot "help":
[1] "output file for processed log fold change matrix"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
[[3]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--library_outfile"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "library_outfile"
Slot "default":
NULL
Slot "help":
[1] "output file for processed library"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
CRISPRcleanR normalisation options
Code
crisprcleanr_normalisation_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--min_reads"
Slot "action":
[1] "store"
Slot "type":
[1] "double"
Slot "dest":
[1] "min_reads"
Slot "default":
[1] 30
Slot "help":
[1] "minimum number of reads for filtering [Default: 30]"
Slot "metavar":
[1] "numeric"
Slot "callback":
NULL
Slot "callback_args":
list()
[[2]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--n_controls"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "n_controls"
Slot "default":
[1] "30"
Slot "help":
[1] "number of control samples"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
CRISPRcleanR correction options
Code
crisprcleanr_correction_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--lfc_matrix"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "lfc_matrix"
Slot "default":
NULL
Slot "help":
[1] "log fold change matrix file"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
[[2]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--no_lfc_header"
Slot "action":
[1] "store_true"
Slot "type":
[1] "logical"
Slot "dest":
[1] "no_lfc_header"
Slot "default":
[1] FALSE
Slot "help":
[1] "fold change file has no header"
Slot "metavar":
character(0)
Slot "callback":
NULL
Slot "callback_args":
list()
[[3]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--lfc_delim"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "lfc_delim"
Slot "default":
[1] "\t"
Slot "help":
[1] "fold change file delimiter [Default: \\t]"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
[[4]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--lfc_id_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "integer"
Slot "dest":
[1] "lfc_id_column_index"
Slot "default":
[1] 1
Slot "help":
[1] "index of id column in fold change matrix [Default: 1]"
Slot "metavar":
[1] "integer"
Slot "callback":
NULL
Slot "callback_args":
list()
[[5]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--lfc_gene_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "integer"
Slot "dest":
[1] "lfc_gene_column_index"
Slot "default":
[1] 2
Slot "help":
[1] "index of gene column in fold change matrix [Default: 2]"
Slot "metavar":
[1] "integer"
Slot "callback":
NULL
Slot "callback_args":
list()
[[6]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--lfc_lfc_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "lfc_lfc_column_index"
Slot "default":
[1] "3"
Slot "help":
[1] "index of columns containing fold change matrix (e.g. 3 or 3,4,5 or 3-5 or 3-5,6-8) [Default: 3]"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
[[7]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--lfc_gene_matrix_outfile"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "lfc_gene_matrix_outfile"
Slot "default":
NULL
Slot "help":
[1] "output file for processed gene-level fold change matrix"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
basic infile options
Code
basic_infile_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--infile"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "infile"
Slot "default":
NULL
Slot "help":
[1] "input file"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
count skip options
Code
count_skip_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--count_skip"
Slot "action":
[1] "store"
Slot "type":
[1] "double"
Slot "dest":
[1] "count_skip"
Slot "default":
[1] 0
Slot "help":
[1] "number of lines to skip when reading file [Default: 0]"
Slot "metavar":
[1] "numeric"
Slot "callback":
NULL
Slot "callback_args":
list()
fold change path options
Code
fold_change_path_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--fold_changes"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "fold_changes"
Slot "default":
NULL
Slot "help":
[1] "path to fold change matrix"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
fold change format options
Code
fold_change_format_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--no_fc_header"
Slot "action":
[1] "store_true"
Slot "type":
[1] "logical"
Slot "dest":
[1] "no_fc_header"
Slot "default":
[1] FALSE
Slot "help":
[1] "fold change file has no header"
Slot "metavar":
character(0)
Slot "callback":
NULL
Slot "callback_args":
list()
[[2]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--fc_delim"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "fc_delim"
Slot "default":
[1] "\t"
Slot "help":
[1] "fold change file delimiter [Default: \\t]"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
fold change column index options
Code
fold_change_column_index_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--fc_id_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "integer"
Slot "dest":
[1] "fc_id_column_index"
Slot "default":
[1] 1
Slot "help":
[1] "index of id column in fold change matrix [Default: 1]"
Slot "metavar":
[1] "integer"
Slot "callback":
NULL
Slot "callback_args":
list()
[[2]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--fc_gene_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "integer"
Slot "dest":
[1] "fc_gene_column_index"
Slot "default":
NULL
Slot "help":
[1] "index of gene column in fold change matrix"
Slot "metavar":
[1] "integer"
Slot "callback":
NULL
Slot "callback_args":
list()
[[3]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--fc_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "fc_column_index"
Slot "default":
NULL
Slot "help":
[1] "index of columns containing fold changes (e.g. 3 or 3,4,5 or 3-5 or 3-5,6-8)"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
generic infile options
Code
infile_format_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--no_infile_header"
Slot "action":
[1] "store_true"
Slot "type":
[1] "logical"
Slot "dest":
[1] "no_infile_header"
Slot "default":
[1] FALSE
Slot "help":
[1] "infile has no header"
Slot "metavar":
character(0)
Slot "callback":
NULL
Slot "callback_args":
list()
[[2]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--infile_delim"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "infile_delim"
Slot "default":
[1] "\t"
Slot "help":
[1] "infile delimiter [Default: \\t]"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
generic infile column index options
Code
infile_column_index_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--infile_id_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "integer"
Slot "dest":
[1] "infile_id_column_index"
Slot "default":
NULL
Slot "help":
[1] "index of id column in infile"
Slot "metavar":
[1] "integer"
Slot "callback":
NULL
Slot "callback_args":
list()
[[2]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--infile_gene_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "integer"
Slot "dest":
[1] "infile_gene_column_index"
Slot "default":
NULL
Slot "help":
[1] "index of gene column in infile matrix"
Slot "metavar":
[1] "integer"
Slot "callback":
NULL
Slot "callback_args":
list()
[[3]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--infile_data_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "infile_data_column_index"
Slot "default":
NULL
Slot "help":
[1] "index of columns containing data for processing in infile (e.g. 3 or 3,4,5 or 3-5 or 3-5,6-8)"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
strip id options
Code
strip_id_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--strip_ids"
Slot "action":
[1] "store_true"
Slot "type":
[1] "logical"
Slot "dest":
[1] "strip_ids"
Slot "default":
[1] FALSE
Slot "help":
[1] "remove period and start sgRNA identifiers with character"
Slot "metavar":
character(0)
Slot "callback":
NULL
Slot "callback_args":
list()
count library outfile options
Code
count_library_outfile_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--count_matrix_outfile"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "count_matrix_outfile"
Slot "default":
NULL
Slot "help":
[1] "output file for count matrix"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
[[2]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--library_outfile"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "library_outfile"
Slot "default":
NULL
Slot "help":
[1] "output file for processed library"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
filtered guide outfile options
Code
filtered_guide_output_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--filtered_guides_outfile"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "filtered_guides_outfile"
Slot "default":
NULL
Slot "help":
[1] "file of guides that were remove"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
sequencing qc options
Code
sequencing_qc_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--low_counts"
Slot "action":
[1] "store"
Slot "type":
[1] "double"
Slot "dest":
[1] "low_counts"
Slot "default":
[1] 30
Slot "help":
[1] "threshold for low counts [Default: 30]"
Slot "metavar":
[1] "numeric"
Slot "callback":
NULL
Slot "callback_args":
list()
[[2]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--no_plot"
Slot "action":
[1] "store_true"
Slot "type":
[1] "logical"
Slot "dest":
[1] "no_plot"
Slot "default":
[1] FALSE
Slot "help":
[1] "do not produce plots"
Slot "metavar":
character(0)
Slot "callback":
NULL
Slot "callback_args":
list()
correltion options
Code
correlation_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--cor_method"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "cor_method"
Slot "default":
[1] "pearson"
Slot "help":
[1] "which correlation coefficient to compute [Default: pearson]"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
intermediate qc options
Code
intermediate_qc_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--is_fc"
Slot "action":
[1] "store_true"
Slot "type":
[1] "logical"
Slot "dest":
[1] "is_fc"
Slot "default":
[1] FALSE
Slot "help":
[1] "whether input is a fold change matrix"
Slot "metavar":
character(0)
Slot "callback":
NULL
Slot "callback_args":
list()
[[2]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--is_gene"
Slot "action":
[1] "store_true"
Slot "type":
[1] "logical"
Slot "dest":
[1] "is_gene"
Slot "default":
[1] FALSE
Slot "help":
[1] "whether input is gene-level"
Slot "metavar":
character(0)
Slot "callback":
NULL
Slot "callback_args":
list()
[[3]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--no_check_names"
Slot "action":
[1] "store_true"
Slot "type":
[1] "logical"
Slot "dest":
[1] "no_check_names"
Slot "default":
[1] FALSE
Slot "help":
[1] "whether to check sample names exist in metadata"
Slot "metavar":
character(0)
Slot "callback":
NULL
Slot "callback_args":
list()
[[4]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--no_plot"
Slot "action":
[1] "store_true"
Slot "type":
[1] "logical"
Slot "dest":
[1] "no_plot"
Slot "default":
[1] FALSE
Slot "help":
[1] "do not produce plots"
Slot "metavar":
character(0)
Slot "callback":
NULL
Slot "callback_args":
list()
BAGEL gene infile options
Code
bagel_gene_infile_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--ess"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "ess"
Slot "default":
NULL
Slot "help":
[1] "file containing essential gene names"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
[[2]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--ess_gene_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "integer"
Slot "dest":
[1] "ess_gene_column_index"
Slot "default":
[1] 1
Slot "help":
[1] "index of column containing gene names in essential gene file [Default: 1]"
Slot "metavar":
[1] "integer"
Slot "callback":
NULL
Slot "callback_args":
list()
[[3]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--no_ess_header"
Slot "action":
[1] "store_true"
Slot "type":
[1] "logical"
Slot "dest":
[1] "no_ess_header"
Slot "default":
[1] FALSE
Slot "help":
[1] "essential gene file has no header"
Slot "metavar":
character(0)
Slot "callback":
NULL
Slot "callback_args":
list()
[[4]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--ess_delim"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "ess_delim"
Slot "default":
[1] "\t"
Slot "help":
[1] "essential gene file delimiter [Default: \\t]"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
[[5]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--noness"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "noness"
Slot "default":
NULL
Slot "help":
[1] "file containing non-essential gene names"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
[[6]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--noness_gene_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "integer"
Slot "dest":
[1] "noness_gene_column_index"
Slot "default":
[1] 1
Slot "help":
[1] "index of column containing gene names in non-essential gene file [Default: 1]"
Slot "metavar":
[1] "integer"
Slot "callback":
NULL
Slot "callback_args":
list()
[[7]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--no_noness_header"
Slot "action":
[1] "store_true"
Slot "type":
[1] "logical"
Slot "dest":
[1] "no_noness_header"
Slot "default":
[1] FALSE
Slot "help":
[1] "non-essential gene file has no header"
Slot "metavar":
character(0)
Slot "callback":
NULL
Slot "callback_args":
list()
[[8]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--noness_delim"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "noness_delim"
Slot "default":
[1] "\t"
Slot "help":
[1] "non-essential gene file delimiter [Default: \\t]"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
scaling options
Code
scaling_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] "-t"
Slot "long_flag":
[1] "--threshold"
Slot "action":
[1] "store"
Slot "type":
[1] "double"
Slot "dest":
[1] "threshold"
Slot "default":
[1] 0.05
Slot "help":
[1] "threshold [Default: 0.05]"
Slot "metavar":
[1] "numeric"
Slot "callback":
NULL
Slot "callback_args":
list()
[[2]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--is_fc"
Slot "action":
[1] "store_true"
Slot "type":
[1] "logical"
Slot "dest":
[1] "is_fc"
Slot "default":
[1] FALSE
Slot "help":
[1] "whether input is a fold change matrix"
Slot "metavar":
character(0)
Slot "callback":
NULL
Slot "callback_args":
list()
[[3]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--is_bf"
Slot "action":
[1] "store_true"
Slot "type":
[1] "logical"
Slot "dest":
[1] "is_bf"
Slot "default":
[1] FALSE
Slot "help":
[1] "whether input is Bayes factors"
Slot "metavar":
character(0)
Slot "callback":
NULL
Slot "callback_args":
list()
[[4]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--no_plot"
Slot "action":
[1] "store_true"
Slot "type":
[1] "logical"
Slot "dest":
[1] "no_plot"
Slot "default":
[1] FALSE
Slot "help":
[1] "do not produce plots"
Slot "metavar":
character(0)
Slot "callback":
NULL
Slot "callback_args":
list()
cancerit/RCRISPR documentation built on April 26, 2023, 10:12 p.m.
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shared output options
Code
shared_output_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] "-r"
Slot "long_flag":
[1] "--rdata"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "rdata"
Slot "default":
NULL
Slot "help":
[1] "output file for .Rdata"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
[[2]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] "-d"
Slot "long_flag":
[1] "--outdir"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "outdir"
Slot "default":
NULL
Slot "help":
[1] "output directory"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
[[3]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] "-p"
Slot "long_flag":
[1] "--prefix"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "prefix"
Slot "default":
NULL
Slot "help":
[1] "output file prefix"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
[[4]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] "-s"
Slot "long_flag":
[1] "--suffix"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "suffix"
Slot "default":
NULL
Slot "help":
[1] "output file suffix"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
basic outfile options
Code
basic_outfile_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] "-o"
Slot "long_flag":
[1] "--outfile"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "outfile"
Slot "default":
NULL
Slot "help":
[1] "output file"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
count path options
Code
count_path_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] "-c"
Slot "long_flag":
[1] "--counts"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "counts"
Slot "default":
NULL
Slot "help":
[1] "path to directory of counts or a count matrix"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
count type options
Code
count_type_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--counts_type"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "counts_type"
Slot "default":
[1] "single"
Slot "help":
[1] "count type (must be either 'single' or 'matrix') [Default: single]"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
count format options
Code
count_format_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--no_counts_header"
Slot "action":
[1] "store_true"
Slot "type":
[1] "logical"
Slot "dest":
[1] "no_counts_header"
Slot "default":
[1] FALSE
Slot "help":
[1] "count file has no header"
Slot "metavar":
character(0)
Slot "callback":
NULL
Slot "callback_args":
list()
[[2]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--counts_delim"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "counts_delim"
Slot "default":
[1] "\t"
Slot "help":
[1] "count file delimiter [Default: \\t]"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
count column index options
Code
count_column_index_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--count_id_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "integer"
Slot "dest":
[1] "count_id_column_index"
Slot "default":
[1] 1
Slot "help":
[1] "index of id column in counts [Default: 1]"
Slot "metavar":
[1] "integer"
Slot "callback":
NULL
Slot "callback_args":
list()
[[2]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--count_gene_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "integer"
Slot "dest":
[1] "count_gene_column_index"
Slot "default":
[1] 2
Slot "help":
[1] "index of gene column in counts [Default: 2]"
Slot "metavar":
[1] "integer"
Slot "callback":
NULL
Slot "callback_args":
list()
[[3]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--count_count_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "count_count_column_index"
Slot "default":
[1] "3"
Slot "help":
[1] "index of columns containing counts (e.g. 3 or 3,4,5 or 3-5 or 3-5,6-8) [Default: 3]"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
library annotation options
Code
library_annotation_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] "-l"
Slot "long_flag":
[1] "--library"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "library"
Slot "default":
NULL
Slot "help":
[1] "library file containing guide identifiers and annotations"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
library annotation format options
Code
library_annotation_format_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--no_library_header"
Slot "action":
[1] "store_true"
Slot "type":
[1] "logical"
Slot "dest":
[1] "no_library_header"
Slot "default":
[1] FALSE
Slot "help":
[1] "library has no header"
Slot "metavar":
character(0)
Slot "callback":
NULL
Slot "callback_args":
list()
[[2]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--library_delim"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "library_delim"
Slot "default":
[1] "\t"
Slot "help":
[1] "library delimiter [Default: \\t]"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
library annotation column index options
Code
library_annotation_column_index_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--library_id_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "integer"
Slot "dest":
[1] "library_id_column_index"
Slot "default":
[1] 1
Slot "help":
[1] "index of column containing guide id in library annotations [Default: 1]"
Slot "metavar":
[1] "integer"
Slot "callback":
NULL
Slot "callback_args":
list()
[[2]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--library_gene_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "integer"
Slot "dest":
[1] "library_gene_column_index"
Slot "default":
[1] 2
Slot "help":
[1] "index of column containing gene name(s) in library annotations"
Slot "metavar":
[1] "integer"
Slot "callback":
NULL
Slot "callback_args":
list()
library annotation genomic column index options
Code
library_annotation_genomic_column_index_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--library_chr_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "library_chr_column_index"
Slot "default":
NULL
Slot "help":
[1] "index of column containing chromosome name in library annotations"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
[[2]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--library_start_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "library_start_column_index"
Slot "default":
NULL
Slot "help":
[1] "index of column containing chromosome start position in library annotations"
Slot "metavar":
[1] "integer"
Slot "callback":
NULL
Slot "callback_args":
list()
[[3]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--library_end_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "library_end_column_index"
Slot "default":
NULL
Slot "help":
[1] "index of column containing chromosome end position in library annotations"
Slot "metavar":
[1] "integer"
Slot "callback":
NULL
Slot "callback_args":
list()
sample metadata options
Code
sample_metadata_options()
sample metadata format options
Code
sample_metadata_format_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--no_info_header"
Slot "action":
[1] "store_true"
Slot "type":
[1] "logical"
Slot "dest":
[1] "no_info_header"
Slot "default":
[1] FALSE
Slot "help":
[1] "sample metadata has no header"
Slot "metavar":
character(0)
Slot "callback":
NULL
Slot "callback_args":
list()
[[2]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--info_delim"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "info_delim"
Slot "default":
[1] "\t"
Slot "help":
[1] "sample metadata delimiter [Default: \\t]"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
sample metadata sample filename options
Code
sample_metadata_sample_filename_column_index_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--info_filename_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "integer"
Slot "dest":
[1] "info_filename_column_index"
Slot "default":
[1] 1
Slot "help":
[1] "index of column containing sample count filename in sample mapping [Default: 1]"
Slot "metavar":
[1] "integer"
Slot "callback":
NULL
Slot "callback_args":
list()
sample metadata sample label options
Code
sample_metadata_sample_label_column_index_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--info_label_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "integer"
Slot "dest":
[1] "info_label_column_index"
Slot "default":
[1] 2
Slot "help":
[1] "index of column containing sample labels in sample mapping [Default: 2]"
Slot "metavar":
[1] "integer"
Slot "callback":
NULL
Slot "callback_args":
list()
sample metadata sample type options
Code
sample_metadata_sample_type_column_index_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--info_plasmid_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "integer"
Slot "dest":
[1] "info_plasmid_column_index"
Slot "default":
NULL
Slot "help":
[1] "index of column indicating whether sample type is plasmid in sample mapping"
Slot "metavar":
[1] "integer"
Slot "callback":
NULL
Slot "callback_args":
list()
[[2]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--info_control_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "integer"
Slot "dest":
[1] "info_control_column_index"
Slot "default":
NULL
Slot "help":
[1] "index of column indicating whether sample type is control in sample mapping"
Slot "metavar":
[1] "integer"
Slot "callback":
NULL
Slot "callback_args":
list()
[[3]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--info_treatment_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "integer"
Slot "dest":
[1] "info_treatment_column_index"
Slot "default":
NULL
Slot "help":
[1] "index of column indicating whether sample type is treatment in sample mapping"
Slot "metavar":
[1] "integer"
Slot "callback":
NULL
Slot "callback_args":
list()
sample metadata sample group options
Code
sample_metadata_sample_group_column_index_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--info_group_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "info_group_column_index"
Slot "default":
NULL
Slot "help":
[1] "index of column containing sample group name in sample mapping"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
sample metadata sample read count options
Code
sample_metadata_sample_read_count_column_index_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--info_reads_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "info_reads_column_index"
Slot "default":
NULL
Slot "help":
[1] "index of column containing sample read counts in sample mapping"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
duplicate guide options
Code
duplicate_guide_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--duplicate_guides_outfile"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "duplicate_guides_outfile"
Slot "default":
NULL
Slot "help":
[1] "output file for duplicate guides"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
remove guide options
Code
remove_guide_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--guides_to_remove"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "guides_to_remove"
Slot "default":
NULL
Slot "help":
[1] "file of guides to remove"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
MAGeCK RRA summary options
Code
mageck_rra_summary_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--gene_summary"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "gene_summary"
Slot "default":
NULL
Slot "help":
[1] "MAGeCK RRA gene summary"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
[[2]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--sgrna_summary"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "sgrna_summary"
Slot "default":
NULL
Slot "help":
[1] "MAGeCK RRA gene summary"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
[[3]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--n_genes"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "n_genes"
Slot "default":
[1] "10"
Slot "help":
[1] "number of genes to label in plots (in each direction)"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
[[4]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] "-f"
Slot "long_flag":
[1] "--fdr"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "fdr"
Slot "default":
[1] "0.05"
Slot "help":
[1] "maximum FDR value"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
BAGEL normalisation options
Code
bagel_normalisation_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--pseudocount"
Slot "action":
[1] "store"
Slot "type":
[1] "double"
Slot "dest":
[1] "pseudocount"
Slot "default":
[1] 5
Slot "help":
[1] "pseudocount to add to sample counts"
Slot "metavar":
[1] "numeric"
Slot "callback":
NULL
Slot "callback_args":
list()
[[2]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--scaling_factor"
Slot "action":
[1] "store"
Slot "type":
[1] "double"
Slot "dest":
[1] "scaling_factor"
Slot "default":
[1] 1e+07
Slot "help":
[1] "scaling factor for normalised counts"
Slot "metavar":
[1] "numeric"
Slot "callback":
NULL
Slot "callback_args":
list()
Calculate LFC options
Code
calculate_lfc_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--sgrna_outfile"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "sgrna_outfile"
Slot "default":
NULL
Slot "help":
[1] "output file for sgRNA-level fold change matrix"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
[[2]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--gene_outfile"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "gene_outfile"
Slot "default":
NULL
Slot "help":
[1] "output file for gene-level fold change matrix"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
[[3]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--count_matrix_outfile"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "count_matrix_outfile"
Slot "default":
NULL
Slot "help":
[1] "output file for count matrix"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
[[4]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--control_indices"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "control_indices"
Slot "default":
NULL
Slot "help":
[1] "pseudocount to add to sample counts"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
[[5]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--treatment_indices"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "treatment_indices"
Slot "default":
NULL
Slot "help":
[1] "scaling factor for normalised counts"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
[[6]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--pseudocount"
Slot "action":
[1] "store"
Slot "type":
[1] "double"
Slot "dest":
[1] "pseudocount"
Slot "default":
[1] 0.5
Slot "help":
[1] "pseudocount to add to sample counts"
Slot "metavar":
[1] "numeric"
Slot "callback":
NULL
Slot "callback_args":
list()
Remove guides with no coordinates options
Code
remove_no_coordinate_guide_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--excluded_guides_outfile"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "excluded_guides_outfile"
Slot "default":
NULL
Slot "help":
[1] "file of guides that were remove"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
Filter counts and library by index options
Code
filter_by_index_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--filter_indices"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "filter_indices"
Slot "default":
NULL
Slot "help":
[1] "column indices to use for filtering"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
[[2]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--filter_method"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "filter_method"
Slot "default":
NULL
Slot "help":
[1] "filter method ( all, any, mean or median ) [Default: all]"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
[[3]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--min_reads"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "min_reads"
Slot "default":
[1] "30"
Slot "help":
[1] "minimum number of reads for filtering [Default: 30]"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
CRISPRcleanR output options
Code
crisprcleanr_output_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--count_matrix_outfile"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "count_matrix_outfile"
Slot "default":
NULL
Slot "help":
[1] "output file for processed count matrix"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
[[2]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--lfc_matrix_outfile"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "lfc_matrix_outfile"
Slot "default":
NULL
Slot "help":
[1] "output file for processed log fold change matrix"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
[[3]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--library_outfile"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "library_outfile"
Slot "default":
NULL
Slot "help":
[1] "output file for processed library"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
CRISPRcleanR normalisation options
Code
crisprcleanr_normalisation_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--min_reads"
Slot "action":
[1] "store"
Slot "type":
[1] "double"
Slot "dest":
[1] "min_reads"
Slot "default":
[1] 30
Slot "help":
[1] "minimum number of reads for filtering [Default: 30]"
Slot "metavar":
[1] "numeric"
Slot "callback":
NULL
Slot "callback_args":
list()
[[2]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--n_controls"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "n_controls"
Slot "default":
[1] "30"
Slot "help":
[1] "number of control samples"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
CRISPRcleanR correction options
Code
crisprcleanr_correction_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--lfc_matrix"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "lfc_matrix"
Slot "default":
NULL
Slot "help":
[1] "log fold change matrix file"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
[[2]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--no_lfc_header"
Slot "action":
[1] "store_true"
Slot "type":
[1] "logical"
Slot "dest":
[1] "no_lfc_header"
Slot "default":
[1] FALSE
Slot "help":
[1] "fold change file has no header"
Slot "metavar":
character(0)
Slot "callback":
NULL
Slot "callback_args":
list()
[[3]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--lfc_delim"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "lfc_delim"
Slot "default":
[1] "\t"
Slot "help":
[1] "fold change file delimiter [Default: \\t]"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
[[4]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--lfc_id_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "integer"
Slot "dest":
[1] "lfc_id_column_index"
Slot "default":
[1] 1
Slot "help":
[1] "index of id column in fold change matrix [Default: 1]"
Slot "metavar":
[1] "integer"
Slot "callback":
NULL
Slot "callback_args":
list()
[[5]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--lfc_gene_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "integer"
Slot "dest":
[1] "lfc_gene_column_index"
Slot "default":
[1] 2
Slot "help":
[1] "index of gene column in fold change matrix [Default: 2]"
Slot "metavar":
[1] "integer"
Slot "callback":
NULL
Slot "callback_args":
list()
[[6]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--lfc_lfc_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "lfc_lfc_column_index"
Slot "default":
[1] "3"
Slot "help":
[1] "index of columns containing fold change matrix (e.g. 3 or 3,4,5 or 3-5 or 3-5,6-8) [Default: 3]"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
[[7]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--lfc_gene_matrix_outfile"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "lfc_gene_matrix_outfile"
Slot "default":
NULL
Slot "help":
[1] "output file for processed gene-level fold change matrix"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
basic infile options
Code
basic_infile_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--infile"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "infile"
Slot "default":
NULL
Slot "help":
[1] "input file"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
count skip options
Code
count_skip_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--count_skip"
Slot "action":
[1] "store"
Slot "type":
[1] "double"
Slot "dest":
[1] "count_skip"
Slot "default":
[1] 0
Slot "help":
[1] "number of lines to skip when reading file [Default: 0]"
Slot "metavar":
[1] "numeric"
Slot "callback":
NULL
Slot "callback_args":
list()
fold change path options
Code
fold_change_path_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--fold_changes"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "fold_changes"
Slot "default":
NULL
Slot "help":
[1] "path to fold change matrix"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
fold change format options
Code
fold_change_format_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--no_fc_header"
Slot "action":
[1] "store_true"
Slot "type":
[1] "logical"
Slot "dest":
[1] "no_fc_header"
Slot "default":
[1] FALSE
Slot "help":
[1] "fold change file has no header"
Slot "metavar":
character(0)
Slot "callback":
NULL
Slot "callback_args":
list()
[[2]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--fc_delim"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "fc_delim"
Slot "default":
[1] "\t"
Slot "help":
[1] "fold change file delimiter [Default: \\t]"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
fold change column index options
Code
fold_change_column_index_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--fc_id_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "integer"
Slot "dest":
[1] "fc_id_column_index"
Slot "default":
[1] 1
Slot "help":
[1] "index of id column in fold change matrix [Default: 1]"
Slot "metavar":
[1] "integer"
Slot "callback":
NULL
Slot "callback_args":
list()
[[2]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--fc_gene_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "integer"
Slot "dest":
[1] "fc_gene_column_index"
Slot "default":
NULL
Slot "help":
[1] "index of gene column in fold change matrix"
Slot "metavar":
[1] "integer"
Slot "callback":
NULL
Slot "callback_args":
list()
[[3]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--fc_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "fc_column_index"
Slot "default":
NULL
Slot "help":
[1] "index of columns containing fold changes (e.g. 3 or 3,4,5 or 3-5 or 3-5,6-8)"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
generic infile options
Code
infile_format_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--no_infile_header"
Slot "action":
[1] "store_true"
Slot "type":
[1] "logical"
Slot "dest":
[1] "no_infile_header"
Slot "default":
[1] FALSE
Slot "help":
[1] "infile has no header"
Slot "metavar":
character(0)
Slot "callback":
NULL
Slot "callback_args":
list()
[[2]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--infile_delim"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "infile_delim"
Slot "default":
[1] "\t"
Slot "help":
[1] "infile delimiter [Default: \\t]"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
generic infile column index options
Code
infile_column_index_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--infile_id_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "integer"
Slot "dest":
[1] "infile_id_column_index"
Slot "default":
NULL
Slot "help":
[1] "index of id column in infile"
Slot "metavar":
[1] "integer"
Slot "callback":
NULL
Slot "callback_args":
list()
[[2]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--infile_gene_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "integer"
Slot "dest":
[1] "infile_gene_column_index"
Slot "default":
NULL
Slot "help":
[1] "index of gene column in infile matrix"
Slot "metavar":
[1] "integer"
Slot "callback":
NULL
Slot "callback_args":
list()
[[3]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--infile_data_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "infile_data_column_index"
Slot "default":
NULL
Slot "help":
[1] "index of columns containing data for processing in infile (e.g. 3 or 3,4,5 or 3-5 or 3-5,6-8)"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
strip id options
Code
strip_id_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--strip_ids"
Slot "action":
[1] "store_true"
Slot "type":
[1] "logical"
Slot "dest":
[1] "strip_ids"
Slot "default":
[1] FALSE
Slot "help":
[1] "remove period and start sgRNA identifiers with character"
Slot "metavar":
character(0)
Slot "callback":
NULL
Slot "callback_args":
list()
count library outfile options
Code
count_library_outfile_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--count_matrix_outfile"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "count_matrix_outfile"
Slot "default":
NULL
Slot "help":
[1] "output file for count matrix"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
[[2]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--library_outfile"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "library_outfile"
Slot "default":
NULL
Slot "help":
[1] "output file for processed library"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
filtered guide outfile options
Code
filtered_guide_output_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--filtered_guides_outfile"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "filtered_guides_outfile"
Slot "default":
NULL
Slot "help":
[1] "file of guides that were remove"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
sequencing qc options
Code
sequencing_qc_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--low_counts"
Slot "action":
[1] "store"
Slot "type":
[1] "double"
Slot "dest":
[1] "low_counts"
Slot "default":
[1] 30
Slot "help":
[1] "threshold for low counts [Default: 30]"
Slot "metavar":
[1] "numeric"
Slot "callback":
NULL
Slot "callback_args":
list()
[[2]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--no_plot"
Slot "action":
[1] "store_true"
Slot "type":
[1] "logical"
Slot "dest":
[1] "no_plot"
Slot "default":
[1] FALSE
Slot "help":
[1] "do not produce plots"
Slot "metavar":
character(0)
Slot "callback":
NULL
Slot "callback_args":
list()
correltion options
Code
correlation_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--cor_method"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "cor_method"
Slot "default":
[1] "pearson"
Slot "help":
[1] "which correlation coefficient to compute [Default: pearson]"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
intermediate qc options
Code
intermediate_qc_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--is_fc"
Slot "action":
[1] "store_true"
Slot "type":
[1] "logical"
Slot "dest":
[1] "is_fc"
Slot "default":
[1] FALSE
Slot "help":
[1] "whether input is a fold change matrix"
Slot "metavar":
character(0)
Slot "callback":
NULL
Slot "callback_args":
list()
[[2]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--is_gene"
Slot "action":
[1] "store_true"
Slot "type":
[1] "logical"
Slot "dest":
[1] "is_gene"
Slot "default":
[1] FALSE
Slot "help":
[1] "whether input is gene-level"
Slot "metavar":
character(0)
Slot "callback":
NULL
Slot "callback_args":
list()
[[3]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--no_check_names"
Slot "action":
[1] "store_true"
Slot "type":
[1] "logical"
Slot "dest":
[1] "no_check_names"
Slot "default":
[1] FALSE
Slot "help":
[1] "whether to check sample names exist in metadata"
Slot "metavar":
character(0)
Slot "callback":
NULL
Slot "callback_args":
list()
[[4]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--no_plot"
Slot "action":
[1] "store_true"
Slot "type":
[1] "logical"
Slot "dest":
[1] "no_plot"
Slot "default":
[1] FALSE
Slot "help":
[1] "do not produce plots"
Slot "metavar":
character(0)
Slot "callback":
NULL
Slot "callback_args":
list()
BAGEL gene infile options
Code
bagel_gene_infile_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--ess"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "ess"
Slot "default":
NULL
Slot "help":
[1] "file containing essential gene names"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
[[2]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--ess_gene_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "integer"
Slot "dest":
[1] "ess_gene_column_index"
Slot "default":
[1] 1
Slot "help":
[1] "index of column containing gene names in essential gene file [Default: 1]"
Slot "metavar":
[1] "integer"
Slot "callback":
NULL
Slot "callback_args":
list()
[[3]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--no_ess_header"
Slot "action":
[1] "store_true"
Slot "type":
[1] "logical"
Slot "dest":
[1] "no_ess_header"
Slot "default":
[1] FALSE
Slot "help":
[1] "essential gene file has no header"
Slot "metavar":
character(0)
Slot "callback":
NULL
Slot "callback_args":
list()
[[4]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--ess_delim"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "ess_delim"
Slot "default":
[1] "\t"
Slot "help":
[1] "essential gene file delimiter [Default: \\t]"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
[[5]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--noness"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "noness"
Slot "default":
NULL
Slot "help":
[1] "file containing non-essential gene names"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
[[6]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--noness_gene_column_index"
Slot "action":
[1] "store"
Slot "type":
[1] "integer"
Slot "dest":
[1] "noness_gene_column_index"
Slot "default":
[1] 1
Slot "help":
[1] "index of column containing gene names in non-essential gene file [Default: 1]"
Slot "metavar":
[1] "integer"
Slot "callback":
NULL
Slot "callback_args":
list()
[[7]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--no_noness_header"
Slot "action":
[1] "store_true"
Slot "type":
[1] "logical"
Slot "dest":
[1] "no_noness_header"
Slot "default":
[1] FALSE
Slot "help":
[1] "non-essential gene file has no header"
Slot "metavar":
character(0)
Slot "callback":
NULL
Slot "callback_args":
list()
[[8]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--noness_delim"
Slot "action":
[1] "store"
Slot "type":
[1] "character"
Slot "dest":
[1] "noness_delim"
Slot "default":
[1] "\t"
Slot "help":
[1] "non-essential gene file delimiter [Default: \\t]"
Slot "metavar":
[1] "character"
Slot "callback":
NULL
Slot "callback_args":
list()
scaling options
Code
scaling_options()
Output
[[1]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] "-t"
Slot "long_flag":
[1] "--threshold"
Slot "action":
[1] "store"
Slot "type":
[1] "double"
Slot "dest":
[1] "threshold"
Slot "default":
[1] 0.05
Slot "help":
[1] "threshold [Default: 0.05]"
Slot "metavar":
[1] "numeric"
Slot "callback":
NULL
Slot "callback_args":
list()
[[2]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--is_fc"
Slot "action":
[1] "store_true"
Slot "type":
[1] "logical"
Slot "dest":
[1] "is_fc"
Slot "default":
[1] FALSE
Slot "help":
[1] "whether input is a fold change matrix"
Slot "metavar":
character(0)
Slot "callback":
NULL
Slot "callback_args":
list()
[[3]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--is_bf"
Slot "action":
[1] "store_true"
Slot "type":
[1] "logical"
Slot "dest":
[1] "is_bf"
Slot "default":
[1] FALSE
Slot "help":
[1] "whether input is Bayes factors"
Slot "metavar":
character(0)
Slot "callback":
NULL
Slot "callback_args":
list()
[[4]]
An object of class "OptionParserOption"
Slot "short_flag":
[1] NA
Slot "long_flag":
[1] "--no_plot"
Slot "action":
[1] "store_true"
Slot "type":
[1] "logical"
Slot "dest":
[1] "no_plot"
Slot "default":
[1] FALSE
Slot "help":
[1] "do not produce plots"
Slot "metavar":
character(0)
Slot "callback":
NULL
Slot "callback_args":
list()
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