Package: MAGNAMWAR 2.0.4

MAGNAMWAR: A Pipeline for Meta-Genome Wide Association

Correlates variation within the meta-genome to target species phenotype variations in meta-genome with association studies. Follows the pipeline described in Chaston, J.M. et al. (2014) <doi:10.1128/mBio.01631-14>.

Authors:Corinne Sexton [aut], John Chaston [aut, cre], Hayden Smith [ctb]

MAGNAMWAR_2.0.4.tar.gz
MAGNAMWAR_2.0.4.zip(r-4.7)MAGNAMWAR_2.0.4.zip(r-4.6)MAGNAMWAR_2.0.4.zip(r-4.5)
MAGNAMWAR_2.0.4.tgz(r-4.6-any)MAGNAMWAR_2.0.4.tgz(r-4.5-any)
MAGNAMWAR_2.0.4.tar.gz(r-4.7-any)MAGNAMWAR_2.0.4.tar.gz(r-4.6-any)
MAGNAMWAR_2.0.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MAGNAMWAR/json (API)

# Install 'MAGNAMWAR' in R:

install.packages('MAGNAMWAR', repos = c('https://johnchaston.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/johnchaston/magnamwar/issues

Datasets:

after_ortho_format - Formatted output of OrthoMCL.
after_ortho_format_grps - Formatted output of OrthoMCL.
joined_mtrx - Final output of join_repset.
joined_mtrx_grps - Final output of join_repset.
mcl_mtrx - Final output of AnalyzeOrthoMCL
mcl_mtrx_grps - Final output of AnalyzeOrthoMCL
pheno_data - Triglyceride (TAG) content of fruit flies dataset.
starv_pheno_data - Starvation rate of fruit flies dataset.

On CRAN:

3.95 score 18 scripts 311 downloads 1 mentions 14 exports 51 dependencies

Last updated from:185046515c. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	156
source / vignettes	OK	181
linux-release-x86_64	OK	150
macos-release-arm64	OK	249
macos-oldrel-arm64	OK	196
windows-devel	OK	122
windows-release	OK	91
windows-oldrel	OK	119
wasm-release	OK	148

Exports:AnalyzeOrthoMCL CalculatePrincipalCoordinates FormatAfterOrtho FormatMCLFastas JoinRepSeq ManhatGrp PDGPlot PDGvOG PhyDataError PrintOGSeqs QQPlotter RASTtoGBK SurvAppendMatrix WriteMCL

Dependencies:ade4 ape bdsmatrix boot calibrate cli codetools coxme digest doParallel dplyr foreach generics glue iterators lattice lifecycle lme4 magrittr MASS Matrix minqa multcomp mvtnorm nlme nloptr pillar pixmap pkgconfig plyr qqman R6 rbibutils Rcpp RcppArmadillo RcppEigen Rdpack reformulas rlang sandwich segmented seqinr sp survival TH.data tibble tidyselect utf8 vctrs withr zoo

Using MAGNAMWAR: a case study with Drosophila melanogaster

Rendered fromusing_mag.Rmdusingknitr::rmarkdown

Last update: 2017-12-13
Started: 2016-07-26

Citation

Development and contributors

Readme and manuals

Help Manual

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