Package: mbQTL 1.13.0

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_1.13.0.tar.gz
mbQTL_1.13.0.zip(r-4.7)mbQTL_1.13.0.zip(r-4.6)mbQTL_1.13.0.zip(r-4.5)
mbQTL_1.13.0.tgz(r-4.6-any)mbQTL_1.13.0.tgz(r-4.5-any)
mbQTL_1.13.0.tar.gz(r-4.7-any)mbQTL_1.13.0.tar.gz(r-4.6-any)
mbQTL_1.13.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
mbQTL/json (API)

# Install 'mbQTL' in R:

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

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

Datasets:

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

On BioConductor:mbQTL-1.13.0(bioc 3.24)mbQTL-1.12.0(bioc 3.23)

snp microbiome wholegenome metagenomics statisticalmethod regression

4.56 score 1 stars 36 scripts 279 downloads 10 exports 63 dependencies

Last updated from:dcb1e5a97f. Checks:1 WARNING, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	167
linux-devel-x86_64	OK	220
source / vignettes	OK	313
linux-release-x86_64	OK	216
macos-release-arm64	OK	143
macos-oldrel-arm64	OK	114
windows-devel	OK	125
windows-release	OK	129
windows-oldrel	OK	150
wasm-release	OK	144

Exports:allToAllProduct coringTaxa histPvalueLm linearTaxaSnp logitPlotSnpTaxa logRegSnpsTaxa mbQtlCorHeatmap metagenomeSeqToMbqtl qqPlotLm taxaSnpCor

Dependencies:backports Biobase BiocGenerics bitops broom caTools cellranger cli codetools cpp11 crayon dplyr farver foreach generics ggplot2 glmnet glue gplots gtable gtools hms isoband iterators KernSmooth labeling lattice lifecycle limma locfit magrittr Matrix MatrixEQTL matrixStats metagenomeSeq pheatmap pillar pkgconfig prettyunits progress purrr R6 RColorBrewer Rcpp RcppEigen readxl rematch rlang S7 scales shape statmod stringi stringr survival tibble tidyr tidyselect utf8 vctrs viridisLite withr Wrench

mbQTL_Vignette

Rendered frommbQTL_Vignette.Rmdusingknitr::rmarkdown

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

Help page	Topics
title 'mbQTL' is a package for microbial QTL/GWAS Analysis	mbQTL-package mbQTL
'allToAllProduct' creates a dataframe of snp and taxa correlations	allToAllProduct
'binarizeMicrobe' binarizes microbe abundace file based on user's cutoff	binarizeMicrobe
'coringTaxa' creates correlation dataframe for taxa	coringTaxa
'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 statistics	linearTaxaSnp
logitPlotSnpTaxa produces bar plots for counts of ref vs alt vs het allells for particular rsID taxa combinations	logitPlotSnpTaxa
'logRegSnpsTaxa' Performs logistic regression analysis between taxa and SNPs and returns concordance statistics	logRegSnpsTaxa
'mbQtlCorHeatmap' for making heatmap for snp, taxa rho values	mbQtlCorHeatmap
'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 dataframe	metagenomeSeqToMbqtl
'mbQTL' "microbiomeAbund" File	microbeAbund
'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 values	qqPlotLm
'RegSnp' creates a dataframe of parsed long snp files	RegSnp
'mbQTL' "SnpFile"	SnpFile
'taxaSnpCor' for estimation of the rho value between snp, taxa correlations across datasets	taxaSnpCor

Package: mbQTL 1.13.0

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

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)