Description Usage Arguments Value
View source: R/create_matrices.r
Given a samples sheet with some metadata, create a big pile of matrices describing the data.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | create_matrices(
sample_sheet = "sample_sheets/all_samples.xlsx",
ident_column = "identtable",
mut_column = "mutationtable",
min_reads = NULL,
min_indexes = NULL,
min_sequencer = 10,
min_position = NULL,
max_position = NULL,
max_mutations_per_read = NULL,
prune_n = TRUE,
excel = NULL,
verbose = TRUE,
plot_order = c("dna_control", "dna_low", "dna_high", "rna_control", "rna_low",
"rna_high"),
savefile = "sample_tables.rda",
overwrite = FALSE
)
|
sample_sheet |
xlsx/csv/whatever file of metadata. |
ident_column |
Column containing the files of reads identical to the template. |
mut_column |
Column containing the files of reads not identical to the template. |
min_reads |
Filter for the minimum number of reads / index. |
min_indexes |
Filter for the minimum numer of indexes / mutation. |
min_sequencer |
Filter defining the minimum number of reads when looking for sequencer-based mutations. |
min_position |
Filter against weird data at the beginning of the template. |
max_position |
Filter against weird data at the end. |
max_mutations_per_read |
Drop reads with more than this number of mutations. |
prune_n |
Remove mutations which are something to N. |
excel |
Save data to this file. |
verbose |
Print information about the running of this function? |
plot_order |
When plotting, force the order to this. |
savefile |
Save the timeconsuming portion to this file. |
overwrite |
If the savefile exists, overwrite it? |
List with lots of matrices of the resulting data.
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