Package demo: mbQTL: An R/Bioconductor Package for Microbial Quantitative Trait Loci Estimation скачать в хорошем качестве

Package demo: mbQTL: An R/Bioconductor Package for Microbial Quantitative Trait Loci Estimation

mbQTL: An R/Bioconductor Package for Microbial Quantitative Trait Loci (QTL) Estimation Author(s): Mercedeh Movassagh,Steven Schiff,Joseph Paulson Affiliation(s): Yale Medical School Motivation: Large studies have begun to collect both host gene expression and microbiome data at scale. This is an exciting time where we are able to estimate the genetic and genomic interactions between host and its microbial community. Coupling host gene expression in healthy and diseased individuals with microbial abundance data and taxonomy promises to shed light on many important problems, including disease development, progression and individual response to therapies. Results: Here we introduce mbQTL, an R package integrating 16S ribosomal (r)RNA sequencing and single nucleotide variation (SNV) data. We describe various statistical methods implemented for identification of SNV and microbe pairs (regressions and correlation based), relevant statistical significance measures, and plot functionality for interpretation.