## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(echo=TRUE) ## ---- eval=TRUE, include=TRUE, message=FALSE, warning=FALSE------------------- library(bigPint) library(edgeR) library(data.table) data(soybean_ir_sub) data = soybean_ir_sub rownames(data) = data[,1] y = DGEList(counts=data[,-1]) group = c(1,1,1,2,2,2) y = DGEList(counts=y, group=group) Group = factor(c(rep("N",3), rep("P",3))) design <- model.matrix(~0+Group, data=y$samples) colnames(design) <- levels(Group) y <- estimateDisp(y, design) fit <- glmFit(y, design) soybean_ir_sub_metrics <- list() for (i in 1:(ncol(fit)-1)){ for (j in (i+1):ncol(fit)){ contrast=rep(0,ncol(fit)) contrast[i]=1 contrast[j]=-1 lrt <- glmLRT(fit, contrast=contrast) lrt <- topTags(lrt, n = nrow(y[[1]]))[[1]] setDT(lrt, keep.rownames = TRUE)[] colnames(lrt)[1] = "ID" lrt <- as.data.frame(lrt) soybean_ir_sub_metrics[[paste0(colnames(fit)[i], "_", colnames(fit)[j])]] <- lrt } } ## ---- eval=TRUE, include=TRUE------------------------------------------------- str(soybean_ir_sub_metrics, strict.width = "wrap") ## ---- eval=TRUE, include=TRUE------------------------------------------------- names(soybean_ir_sub_metrics) ## ---- eval=TRUE, include=TRUE------------------------------------------------- library(edgeR) library(data.table) data(soybean_cn_sub) data = soybean_cn_sub rownames(data) = data[,1] y = DGEList(counts=data[,-1]) group = c(1,1,1,2,2,2,3,3,3) y = DGEList(counts=y, group=group) Group = factor(c(rep("S1",3), rep("S2",3), rep("S3",3))) design <- model.matrix(~0+Group, data=y$samples) colnames(design) <- levels(Group) y <- estimateDisp(y, design) fit <- glmFit(y, design) soybean_cn_sub_metrics <- list() for (i in 1:(ncol(fit)-1)){ for (j in (i+1):ncol(fit)){ contrast=rep(0,ncol(fit)) contrast[i]=1 contrast[j]=-1 lrt <- glmLRT(fit, contrast=contrast) lrt <- topTags(lrt, n = nrow(y[[1]]))[[1]] setDT(lrt, keep.rownames = TRUE)[] colnames(lrt)[1] = "ID" lrt <- as.data.frame(lrt) soybean_cn_sub_metrics[[paste0(colnames(fit)[i], "_", colnames(fit)[j])]] <- lrt } } ## ---- eval=TRUE, include=TRUE------------------------------------------------- str(soybean_cn_sub_metrics, strict.width = "wrap") ## ---- eval=TRUE, include=TRUE------------------------------------------------- names(soybean_cn_sub_metrics)