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])))