MAGNAMWAR (version 2.0.4)

JoinRepSeq: Join Representative Sequences

Description

Joins the OrthoMCL output matrix to representative sequences

Usage

JoinRepSeq(mcl_data, fa_dir, mcl_mtrx, fastaformat = "new")

Arguments

mcl_data

output of FormatAfterOrtho; a list of matrices; (1) a presence/absence matrix of taxa per OG, (2) a list of the specific protein ids within each OG

fa_dir

Path to the directory where all raw GenBank files are stored. Note, all file names must be changed to a 4-letter code representing each species and have '.fasta' file descriptor

mcl_mtrx

OrthoMCL output matrix from AnalyzeOrthoMCL()

fastaformat

options: new & old; new = no GI numbers included; defaults to new

Value

Returns the original OrthoMCL output matrix with additional columns: representative sequence taxon, representative sequence id, representative sequence annotation, representative sequence

Examples

# NOT RUN {
# }
# NOT RUN {
dir <- system.file('extdata', 'fasta_dir', package='MAGNAMWAR')
dir <- paste(dir,'/',sep='')
joined_mtrx_grps <- JoinRepSeq(after_ortho_format_grps, dir, mcl_mtrx_grps, fastaformat = 'old')
# }