FormatAfterOrtho {MAGNAMWAR} | R Documentation |
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')
[Package MAGNAMWAR version 2.0.4 Index]