Genome-wide pairwise inference of synonymous versus non-synonymous substitution rates (dnds) across multiple subject organisms

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.

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 = ";",
  ...
)

Arguments

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. format = "fasta", format = "gbk". See import_proteome for more details.
ortho_detection	a character string specifying the orthology inference method that shall be performed to detect orthologous genes. Options are: ortho_detection ="DIAMOND-BH": DIAMOND unidirectional best hit. ortho_detection = "DIAMOND-RBH": DIAMOND reciprocal/bidirectional best hit (default).
delete_corrupt_cds	a logical value indicating whether sequences with corrupt base triplets should be removed from the input file. This is the case when the length of coding sequences cannot be divided by 3 and thus the coding sequence contains at least one corrupt base triplet.
store_locally	a logical value indicating whether or not alignment files shall be stored locally rather than in tempdir().
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. sensitivity_mode = "fast" : fastest alignment mode, but least sensitive (default). Designed for finding hits of >70 sensitivity_mode = "mid-sensitive" : fast alignments between the fast mode and the sensitive mode in sensitivity. sensitivity_mode = "sensitive" : fast alignments, but full sensitivity for hits >40 sensitivity_mode = "more-sensitive" : more sensitive than the sensitive mode. sensitivity_mode = "very-sensitive" : sensitive alignment mode. sensitivity_mode = "ultra-sensitive" : most sensitive alignment mode (sensitivity as high as BLASTP).
out_format	a character string specifying the format of the file in which the DIAMOND results shall be stored. Available options are: out_format = "pair" : Pairwise out_format = "xml" : XML out_format = "csv" : Comma-separated file
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 max_target_seqs selects best hits based on the database entry and not by the best e-value. See details here: https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty833/5106166 .
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 db_hard_mask = TRUE.
diamond_exec_path	a path to the DIAMOND executable or conda/miniconda folder.
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_make_options = "--taxonnames" (Default is add_diamond_options = NULL).
add_diamond_options	a character string specifying additional diamond options that shall be passed on to the diamond command line call, e.g. add_diamond_options = "--block-size 4.0 --compress 1 --no-self-hits" (Default is add_diamond_options = NULL).
min_qry_coverage_hsp	minimum qcovhsp (= query coverage of the HSP) of an orthologous hit (a value between 1 and 100).
min_qry_perc_identity	minimum perc_identity (= percent sequence identity between query and selected HSP) of an orthologous hit (a value between 1 and 100).
aa_aln_type	a character string specifying the amino acid alignement type: aa_aln_type = "multiple" or aa_aln_type = "pairwise". Default is aa_aln_type = "pairwise".
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 codon_aln_tool = "pal2nal". Right now only "pal2nal" can be selected as codon alignment tool.
dnds_estimation	a character string specifying the dnds estimation method, e.g. dnds_estimation = "Li" (default).
progress_bar	should a progress bar be shown. Default is progress_bar = TRUE.
diamond_hit_tables	a file path to a folder where DIAMOND hit tables internally generated with diamond_best_hits or diamond_reciprocal_best_hits will be stored.
sep	a file separator that is used to store maps as csv file.
...	additional parameters that shall be passed to dnds.

Details

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.

See also

dnds, import_dnds_across_multiple_species, import_dnds_tbl

Author

Hajk-Georg Drost

Examples

if (FALSE) {
# 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
)
}