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)
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