Description Usage Arguments Details Author(s) See Also Examples
View source: R/dnds_across_multiple_species.R
This function allows you to compute dnds maps between a query organism and a set subject organisms stored in the same folder. The corresponding dnds maps are then stored in an output folder.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 | dnds_across_multiple_species(
query,
subjects_folder,
output_folder,
format = "fasta",
ortho_detection = "DIAMOND-RBH",
delete_corrupt_cds = FALSE,
store_locally = FALSE,
sensitivity_mode = "ultra-sensitive",
out_format = "csv",
evalue = "1E-5",
max_target_seqs = 5000,
cores = 1,
hard_mask = TRUE,
diamond_exec_path = NULL,
add_makedb_options = NULL,
add_diamond_options = NULL,
min_qry_coverage_hsp = 50,
min_qry_perc_identity = 10,
aa_aln_type = "pairwise",
aa_aln_tool = "NW",
codon_aln_tool = "pal2nal",
dnds_estimation = "Li",
progress_bar = TRUE,
diamond_hit_tables = file.path(output_folder, "diamond_hit_tables"),
sep = ";",
...
)
|
query |
a character string specifying the path to the CDS file of the query organism. |
subjects_folder |
a character string specifying the path to the folder where CDS files of the subject organisms are stored. |
output_folder |
a character string specifying the path to the folder where output dnds maps should be stored. |
format |
a character string specifying the file format of the sequence file, e.g. |
ortho_detection |
a character string specifying the orthology inference method that shall be performed to detect orthologous genes. Options are:
|
delete_corrupt_cds |
a logical value indicating whether sequences with corrupt base triplets should be removed from the input |
store_locally |
a logical value indicating whether or not alignment files shall be stored locally rather than in |
sensitivity_mode |
specify the level of alignment sensitivity. The higher the sensitivity level, the more deep homologs can be found, but at the cost of reduced computational speed.
|
out_format |
a character string specifying the format of the file in which the DIAMOND results shall be stored. Available options are:
|
evalue |
a character string specifying the e-value for DIAMOND based orthology inference that is performed in the process of dnds computations. Please use the scientific notation. |
max_target_seqs |
maximum number of aligned sequences that shall be retained. Please be aware that |
cores |
number of computing cores that shall be used to perform parallelized computations. |
hard_mask |
shall low complexity regions be hard masked with TANTAN? Default is |
diamond_exec_path |
a path to the DIAMOND executable or |
add_makedb_options |
a character string specifying additional makedb options that shall be passed on to the diamond makedb command line call, e.g. |
add_diamond_options |
a character string specifying additional diamond options that shall be passed on to the diamond command line call, e.g. |
min_qry_coverage_hsp |
minimum |
min_qry_perc_identity |
minimum |
aa_aln_type |
a character string specifying the amino acid alignement type: |
aa_aln_tool |
a character string specifying the program that should be used e.g. "clustalw". |
codon_aln_tool |
a character string specifying the codon alignment tool that shall be used.
Default is |
dnds_estimation |
a character string specifying the dnds estimation method, e.g. |
progress_bar |
should a progress bar be shown. Default is |
diamond_hit_tables |
a file path to a folder where DIAMOND hit tables internally generated with |
sep |
a file separator that is used to store maps as csv file. |
... |
additional parameters that shall be passed to |
Given a query organism and a set of subject organisms that are stored in the same folder, this function crawls through all subject organism and as a first step computes the pairwise dnds Maps between query and subject organism and as a second step stores the corresponding Map in an output folder.
Hajk-Georg Drost
dnds
, import_dnds_across_multiple_species
, import_dnds_tbl
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 | ## Not run:
# running dnds across several species
dnds_across_multiple_species(
query = system.file('seqs/ortho_thal_cds.fasta', package = 'homologr'),
subjects_folder = system.file('seqs/map_gen_example', package = 'homologr'),
aa_aln_type = "pairwise",
aa_aln_tool = "NW",
codon_aln_tool = "pal2nal",
dnds_estimation = "Li",
output_folder = "homologr_dnds_maps",
quiet = TRUE,
cores = 1
)
# running dnds across several species using DIAMOND executable
# path '/opt/miniconda3/bin/'
dnds_across_multiple_species(
query = system.file('seqs/ortho_thal_cds.fasta', package = 'homologr'),
subjects_folder = system.file('seqs/map_gen_example', package = 'homologr'),
diamond_exec_path = "/opt/miniconda3/bin/",
aa_aln_type = "pairwise",
aa_aln_tool = "NW",
codon_aln_tool = "pal2nal",
dnds_estimation = "Li",
output_folder = "homologr_dnds_maps",
quiet = TRUE,
cores = 1
)
## End(Not run)
|
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