mbQTL: A package for SNP-Taxa mGWAS analysis

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Documentation for package ‘mbQTL’ version 1.4.0

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mbQTL-package title 'mbQTL' is a package for microbial QTL/GWAS Analysis
allToAllProduct 'allToAllProduct' creates a dataframe of snp and taxa correlations
binarizeMicrobe 'binarizeMicrobe' binarizes microbe abundace file based on user's cutoff
coringTaxa 'coringTaxa' creates correlation dataframe for taxa
CovFile 'mbQTL' "CovFile"
histPvalueLm 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.
linearTaxaSnp linearTaxaSnp Performs linear regression analysis between taxa and SNPs and returns concordance statistics
logitPlotSnpTaxa logitPlotSnpTaxa produces bar plots for counts of ref vs alt vs het allells for particular rsID taxa combinations
logRegSnpsTaxa 'logRegSnpsTaxa' Performs logistic regression analysis between taxa and SNPs and returns concordance statistics
mbQTL title 'mbQTL' is a package for microbial QTL/GWAS Analysis
mbQtlCorHeatmap 'mbQtlCorHeatmap' for making heatmap for snp, taxa rho values
metagenomeSeqObj 'mbQTL' "metagenomeSeqObj" "MetagenomSeqObj" is an 'MRexperiment' object format of the "microbeAbund" file.
metagenomeSeqToMbqtl Written by Mercedeh Movassagh mercedeh@ds.dfci.harvard.edu, January 2023: metagenomeSeqToMbqtl Converts metagenomeSeq obj to compatible taxa dataframe
microbeAbund 'mbQTL' "microbiomeAbund" File
prepareCorData 'prepareCorData' prpares and joins snp-taxa and taxa-taxa correlation file.
qqPlotLm 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 values
RegSnp 'RegSnp' creates a dataframe of parsed long snp files
SnpFile 'mbQTL' "SnpFile"
taxaSnpCor 'taxaSnpCor' for estimation of the rho value between snp, taxa correlations across datasets