## ---- 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

## ---- fig.cap="An example ggplot created from a melted SE.", fig.height=5-----
d <- meltSE(SE, genes=row.names(SE)[1:4])
head(d)
suppressPackageStartupMessages(library(ggplot2))
ggplot(d, aes(Condition, counts, fill=Condition)) + geom_violin() + 
    facet_wrap(~feature, scale="free")

## -----------------------------------------------------------------------------
SE <- log2FC(SE, fromAssay="logcpm", controls=SE$Condition=="Homecage")

## ----sessionInfo, echo=FALSE--------------------------------------------------
sessionInfo()