## ----include=FALSE------------------------------------------------------------ library(BiocStyle) ## ----eval=FALSE--------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("SEtools") ## ----eval=FALSE--------------------------------------------------------------- # BiocManager::install("plger/SEtools") ## ----------------------------------------------------------------------------- suppressPackageStartupMessages({ library(SummarizedExperiment) library(SEtools) }) data("SE", package="SEtools") SE ## ----------------------------------------------------------------------------- se1 <- SE[,1:10] se2 <- SE[,11:20] se3 <- mergeSEs( list(se1=se1, se2=se2) ) se3 ## ----------------------------------------------------------------------------- se3 <- mergeSEs( list(se1=se1, se2=se2), do.scale=FALSE) ## ----------------------------------------------------------------------------- se3 <- mergeSEs( list(se1=se1, se2=se2), use.assays=c("counts", "logcpm"), do.scale=c(FALSE, TRUE)) ## ----merging------------------------------------------------------------------ rowData(se1)$metafeature <- sample(LETTERS,nrow(se1),replace = TRUE) rowData(se2)$metafeature <- sample(LETTERS,nrow(se2),replace = TRUE) se3 <- mergeSEs( list(se1=se1, se2=se2), do.scale=FALSE, mergeBy="metafeature", aggFun=median) sechm::sechm(se3, features=row.names(se3)) ## ----aggregating-------------------------------------------------------------- se1b <- aggSE(se1, by = "metafeature") se1b ## ----------------------------------------------------------------------------- SE <- log2FC(SE, fromAssay="logcpm", controls=SE$Condition=="Homecage") ## ----sessionInfo, echo=FALSE-------------------------------------------------- sessionInfo()