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Generate dNdS Maps Between a Query Organism and Multiple Subject Organisms

Source: R/map.generator.R
map_generator_dnds.Rd

This function allows you to compute dNdS or DS Maps between a query organism and a set subject organisms stored in the same folder. The corresponding dNdS/DS Maps are then stored in an output folder.

Usage

map_generator_dnds(
  query_file,
  subjects_folder,
  output_folder,
  eval = "1E-5",
  min_qry_coverage_hsp = 50,
  min_qry_perc_identity = 30,
  ortho_detection = "RBH",
  aa_aln_type = "pairwise",
  aa_aln_tool = "NW",
  codon_aln_tool = "pal2nal",
  dnds_est_method = "Comeron",
  comp_cores = 1,
  progress_bar = TRUE,
  sep = ";",
  ...
)

Arguments

query_file

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/DS Maps should be stored.

eval

a character string specifying the e-value for BLAST based Orthology Inference that is performed in the process of dNdS computations. Please use the scientific notation.

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).

ortho_detection

a character string specifying the Orthology Inference method that shall be used to perform dNdS computations. Possible options are: ortho_detection = "BH" (BLAST best hit), ortho_detection = "RBH" (BLAST best reciprocal hit), etc.

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_est_method

a character string specifying the dNdS estimation method, e.g. "Comeron","Li", "YN", etc. See Details for all options.

comp_cores

number of computing cores that shall be used to perform parallelized computations.

progress_bar

should a progress bar be shown. Default is progress_bar = TRUE.

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 organsisms that are stored in the same folder, this function crawls through all subject organsism and as a first step computes the pairwise dNdS Maps between query and subject organsim and as a second step stores the corresponding Map in an output folder.

Author

Hajk-Georg Drost

Examples

if (FALSE) { # \dontrun{
map_generator_dnds(
   query_file      = system.file('seqs/ortho_thal_cds.fasta', package = 'orthologr'),
   subjects_folder = system.file('seqs/map_gen_example', package = 'orthologr'),
   aa_aln_type      = "pairwise",
   aa_aln_tool      = "NW", 
   codon_aln_tool   = "pal2nal", 
   dnds_est_method  = "Comeron",
   output_folder   = "orthologr_dnds_maps",
   quiet           = TRUE,
   comp_cores      = 1
)

} # }