# mbQTL: A package for SNP-Taxa mGWAS analysis

## Documentation for package ‘mbQTL’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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