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MAGNAMWAR

MAGNAMWAR is used to simplify MGWAS and BGWAS pipelines. It correlates variation within the meta-genome to target species phenotype variations in meta-genome with association studies. For more information and a case study, view the attached vignette.

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Version

Install

install.packages('MAGNAMWAR')

Monthly Downloads

191

Version

2.0.4

License

MIT + file LICENSE

Maintainer

John Chaston

Last Published

July 12th, 2018

Functions in MAGNAMWAR (2.0.4)

starv_pheno_data

Starvation rate of fruit flies dataset.
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
FormatMCLFastas

Format all raw GenBank fastas to single OrthoMCL compatible fasta file
PrintOGSeqs

Print OG Sequences
CalculatePrincipalCoordinates

Show Principal Components Breakdown
FormatAfterOrtho

Format file from output of OrthoMCL algorithm before use in AnalyzeOrthoMCL
AnalyzeOrthoMCL

Main OrthoMCL Analysis
joined_mtrx

Final output of join_repset.
QQPlotter

QQPlot
ManhatGrp

Manhattan Plot of All Taxa
PhyDataError

Phylogenetic Tree with Attached Bar Plot and Standard Error Bars
after_ortho_format

Formatted output of OrthoMCL.
RASTtoGBK

Write RAST files to Genbank formats OrthoMCL Analysis
JoinRepSeq

Join Representative Sequences
joined_mtrx_grps

Final output of join_repset.
pheno_data

Triglyceride (TAG) content of fruit flies dataset.
after_ortho_format_grps

Formatted output of OrthoMCL.
SurvAppendMatrix

Append Survival Test Outputs
WriteMCL

Print analyzed matrix