setup_prev | R Documentation |
Function is useful when number of samples makes manual selection with
diff_expr
error prone and time-consuming. This is often true
for large clinical data sets.
setup_prev(eset, contrasts)
eset |
List containing one expression set with pData 'group' and 'pair'
(optional) columns. Name of |
contrasts |
Character vector specifying contrasts to analyse. Each
contrast must take the form "B-A" where both "B" and "A" are present in
|
List containing necessary information for prev_anal
parameter
of diff_expr
.
library(lydata)
library(Biobase)
# location of raw data
data_dir <- system.file("extdata", package = "lydata")
# load eset
gse_name <- c("GSE34817")
eset <- load_raw(gse_name, data_dir)
# inspect pData of eset
# View(pData(eset$GSE34817)) # if using RStudio
head(pData(eset$GSE34817)) # otherwise
# get group info from pData (differs based on eset)
group <- pData(eset$GSE34817)$characteristics_ch1.1
# make group names concise and valid
group <- gsub("treatment: ", "", group)
group <- make.names(group)
# add group to eset pData
pData(eset$GSE34817)$group <- group
# setup selections
sel <- setup_prev(eset, contrasts = "LY-DMSO")
# run differential expression analysis
anal <- diff_expr(eset, data_dir, prev_anal = sel)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.