Package: mbQTL 1.5.0

Mercedeh Movassagh

mbQTL: mbQTL: A package for SNP-Taxa mGWAS analysis

mbQTL is a statistical R package for simultaneous 16srRNA,16srDNA (microbial) and variant, SNP, SNV (host) relationship, correlation, regression studies. We apply linear, logistic and correlation based statistics to identify the relationships of taxa, genus, species and variant, SNP, SNV in the infected host. We produce various statistical significance measures such as P values, FDR, BC and probability estimation to show significance of these relationships. Further we provide various visualization function for ease and clarification of the results of these analysis. The package is compatible with dataframe, MRexperiment and text formats.

Authors:Mercedeh Movassagh [aut, cre], Steven Schiff [aut], Joseph N Paulson [aut]

mbQTL_1.5.0.tar.gz
mbQTL_1.5.0.zip(r-4.5)mbQTL_1.5.0.zip(r-4.4)mbQTL_1.5.0.zip(r-4.3)
mbQTL_1.5.0.tgz(r-4.4-any)mbQTL_1.5.0.tgz(r-4.3-any)
mbQTL_1.5.0.tar.gz(r-4.5-noble)mbQTL_1.5.0.tar.gz(r-4.4-noble)
mbQTL_1.5.0.tgz(r-4.4-emscripten)mbQTL_1.5.0.tgz(r-4.3-emscripten)
mbQTL.pdf |mbQTL.html✨
mbQTL/json (API)
NEWS

# Install 'mbQTL' in R:
install.packages('mbQTL', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/mercedeh66/mbqtl/issues

Datasets:
  • CovFile - 'mbQTL' "CovFile"
  • SnpFile - 'mbQTL' "SnpFile"
  • metagenomeSeqObj - 'mbQTL' "metagenomeSeqObj" "MetagenomSeqObj" is an 'MRexperiment' object format of the "microbeAbund" file.
  • microbeAbund - 'mbQTL' "microbiomeAbund" File

On BioConductor:mbQTL-1.5.0(bioc 3.20)mbQTL-1.4.0(bioc 3.19)

bioconductor-package

10 exports 0.49 score 68 dependencies

Last updated 2 months agofrom:4fe6777510

Exports:allToAllProductcoringTaxahistPvalueLmlinearTaxaSnplogitPlotSnpTaxalogRegSnpsTaxambQtlCorHeatmapmetagenomeSeqToMbqtlqqPlotLmtaxaSnpCor

Dependencies:backportsBiobaseBiocGenericsbitopsbroomcaToolscellrangerclicodetoolscolorspacecpp11crayondplyrfansifarverforeachgenericsggplot2glmnetgluegplotsgtablegtoolshmsisobanditeratorsKernSmoothlabelinglatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixEQTLmatrixStatsmetagenomeSeqmgcvmunsellnlmepheatmappillarpkgconfigprettyunitsprogresspurrrR6RColorBrewerRcppRcppEigenreadxlrematchrlangscalesshapestatmodstringistringrsurvivaltibbletidyrtidyselectutf8vctrsviridisLitewithrWrench

mbQTL_Vignette

Mercedeh Movassagh

Rendered frommbQTL_Vignette.Rmdusingknitr::rmarkdownon Jun 26 2024.

Last update: 2023-08-16
Started: 2023-01-08

Readme and manuals

Help Manual

Help pageTopics
title 'mbQTL' is a package for microbial QTL/GWAS AnalysismbQTL-package mbQTL
'allToAllProduct' creates a dataframe of snp and taxa correlationsallToAllProduct
'binarizeMicrobe' binarizes microbe abundace file based on user's cutoffbinarizeMicrobe
'coringTaxa' creates correlation dataframe for taxacoringTaxa
'mbQTL' "CovFile"CovFile
histPvalueLm a histogram of Taxa and SNP linear regression analysis. This function creates a histogram object of all SNPs with all taxa Linear regression analysis p values.histPvalueLm
linearTaxaSnp Performs linear regression analysis between taxa and SNPs and returns concordance statisticslinearTaxaSnp
logitPlotSnpTaxa produces bar plots for counts of ref vs alt vs het allells for particular rsID taxa combinationslogitPlotSnpTaxa
'logRegSnpsTaxa' Performs logistic regression analysis between taxa and SNPs and returns concordance statisticslogRegSnpsTaxa
'mbQtlCorHeatmap' for making heatmap for snp, taxa rho valuesmbQtlCorHeatmap
'mbQTL' "metagenomeSeqObj" "MetagenomSeqObj" is an 'MRexperiment' object format of the "microbeAbund" file.metagenomeSeqObj
Written by Mercedeh Movassagh [email protected], January 2023: metagenomeSeqToMbqtl Converts metagenomeSeq obj to compatible taxa dataframemetagenomeSeqToMbqtl
'mbQTL' "microbiomeAbund" FilemicrobeAbund
'prepareCorData' prpares and joins snp-taxa and taxa-taxa correlation file.prepareCorData
qqPlotLm creates QQ-Plot of all SNPs with all taxa Linear regression analysis This function creates QQ-Plot object of all SNPs with all taxa Linear regression analysis of expected versus observed P valuesqqPlotLm
'RegSnp' creates a dataframe of parsed long snp filesRegSnp
'mbQTL' "SnpFile"SnpFile
'taxaSnpCor' for estimation of the rho value between snp, taxa correlations across datasetstaxaSnpCor