JoinRepSeq: Join Representative Sequences
In coripenrod/MAGNAMWAR: A Pipeline for Meta-Genome Wide Association

Description Usage Arguments Value Examples

Joins the OrthoMCL output matrix to representative sequences

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

`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

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

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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')