| collapseReplicates {DESeq2} | R Documentation |
Collapses the columns in object by summing within
levels of a grouping factor groupby. Optionally
renames the columns of returned object with the levels of
the grouping factor. Note: this function is written very
simply and can be easily altered to produce other behavior
by examining the source code.
collapseReplicates(object, groupby, run, renameCols = TRUE)
object |
A |
groupby |
a grouping factor, as long as the columns of object |
run |
optional, the names of each unique column in
object. if provided, a new column |
renameCols |
whether to rename the columns of the returned object using the levels of the grouping factor |
the object with as many columns as levels in
groupby. This object has assay/count data which is
summed from the various columns which are grouped together,
and the colData is subset using the first column for
each group in groupby.
dds <- makeExampleDESeqDataSet(m=12)
# make data with two technical replicates for three samples
dds$sample <- factor(sample(paste0("sample",rep(1:9, c(2,1,1,2,1,1,2,1,1)))))
dds$run <- paste0("run",1:12)
ddsColl <- collapseReplicates(dds, dds$sample, dds$run)
# examine the colData and column names of the collapsed data
colData(ddsColl)
colnames(ddsColl)
# check that the sum of the counts for "sample1" is the same
# as the counts in the "sample1" column in ddsColl
matchFirstLevel <- dds$sample == levels(dds$sample)[1]
stopifnot(all(rowSums(counts(dds[,matchFirstLevel])) == counts(ddsColl[,1])))