## ----setup, include=F, message=F---------------------------------------------- knitr::opts_chunk$set(echo = TRUE) require(metagenomeSeq) require(edgeR) require(Wrench) require(DESeq2) ## ----getPackage, eval=FALSE--------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("Wrench") ## ----eval = FALSE------------------------------------------------------------- # BiocManager::install(“HCBravoLab/Wrench”) ## ----Load, message=FALSE------------------------------------------------------ library(Wrench) ## ----warning=FALSE------------------------------------------------------------ #extract count and group information for from the mouse microbiome data in the metagenomeSeq package data(mouseData) mouseData counts <- MRcounts( mouseData, norm=FALSE ) #get the counts counts[1:10,1:2] group <- pData(mouseData)$diet #get the group/condition vector head(group) #Running wrench with defaults W <- wrench( counts, condition=group ) compositionalFactors <- W$ccf normalizationFactors <- W$nf head( compositionalFactors ) #one factor for each sample head( normalizationFactors) #one factor for each sample ## ----warning=FALSE------------------------------------------------------------ # -- If using metagenomeSeq normalizedObject <- mouseData #mouseData is already a metagenomeSeq object normFactors(normalizedObject) <- normalizationFactors # -- If using edgeR, we must pass in the compositional factors edgerobj <- edgeR::DGEList( counts=counts, group = as.matrix(group), norm.factors=compositionalFactors ) # -- If using DESeq/DESeq2 deseq.obj <- DESeq2::DESeqDataSetFromMatrix(countData = counts, DataFrame(group), ~ group ) deseq.obj sizeFactors(deseq.obj) <- normalizationFactors ## ----warning=FALSE------------------------------------------------------------ time <- as.numeric(as.character(pData(mouseData)$relativeTime)) time.levs <- cut( time, breaks = c(0, 6, 28, 42, 56, 70) ) overall_group <- paste( group, time.levs ) #merge the time information and the group information together W <- wrench( counts, condition = overall_group ) ## ----sessionInfo-------------------------------------------------------------- sessionInfo()