FormatAfterOrtho {MAGNAMWAR}

Format file from output of OrthoMCL algorithm before use in AnalyzeOrthoMCL

Description

After running OrthoMCL and/or submitting to www.orthomcl.org, formats the output file to be used in AnalyzeOrthoMCL

Usage

FormatAfterOrtho(file, format = "ortho")

Arguments

file

Path to the OrthoMCL output file

format

Specification of the method by which file was obtained: defaults to 'ortho' for output from orthomcl.org. Other option is 'groups' for output from local run of OrthoMCL software.

Value

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

Examples

file <- system.file('extdata', 'orthologGroups.txt', package='MAGNAMWAR')
after_ortho_format <- FormatAfterOrtho(file)

file_grps <- system.file('extdata', 'groups_example_r.txt', package='MAGNAMWAR')
after_ortho_format_grps <- FormatAfterOrtho(file_grps, format = 'groups')