A Pipeline for Meta-Genome Wide Association
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Documentation for package ‘MAGNAMWAR’ version 2.0.4
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 |