FormatAfterOrtho: Format file from output of OrthoMCL algorithm before use in...
In coripenrod/MAGNAMWAR: A Pipeline for Meta-Genome Wide Association

Description Usage Arguments Value Examples

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

1	FormatAfterOrtho(file, format = "ortho")

`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.

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

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')