# A Pipeline for Meta-Genome Wide Association

## Documentation for package ‘MAGNAMWAR’ version 2.0.4

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

after_ortho_format | Formatted output of OrthoMCL.
after_ortho_format_grps | Formatted output of OrthoMCL.
AnalyzeOrthoMCL | Main OrthoMCL Analysis
CalculatePrincipalCoordinates | Show Principal Components Breakdown
FormatAfterOrtho | Format file from output of OrthoMCL algorithm before use in AnalyzeOrthoMCL
FormatMCLFastas | Format all raw GenBank fastas to single OrthoMCL compatible fasta file
joined_mtrx | Final output of join_repset.
joined_mtrx_grps | Final output of join_repset.
JoinRepSeq | Join Representative Sequences
ManhatGrp | Manhattan Plot of All Taxa
mcl_mtrx | Final output of AnalyzeOrthoMCL
mcl_mtrx_grps | Final output of AnalyzeOrthoMCL
PDGPlot | Plot of a PDG and Data with Standard Error Bars
PDGvOG | Number of PDGs vs OGs/PDG
pheno_data | Triglyceride (TAG) content of fruit flies dataset.
PhyDataError | Phylogenetic Tree with Attached Bar Plot and Standard Error Bars
PrintOGSeqs | Print OG Sequences
QQPlotter | QQPlot
RASTtoGBK | Write RAST files to Genbank formats OrthoMCL Analysis
starv_pheno_data | Starvation rate of fruit flies dataset.
SurvAppendMatrix | Append Survival Test Outputs
WriteMCL | Print analyzed matrix