subsetSCERows {singleCellTK} | R Documentation |
Used to peform subsetting of a
SingleCellExperiment object using a variety of methods that
indicate the correct rows to keep. The various methods,
index
, bool
, and rowData
, can be used in conjunction
with one another. If returnAsAltExp
is set to TRUE
,
then the returned object will have the same number of rows as the input
inSCE
as the subsetted object will be stored in the
altExp
slot.
subsetSCERows( inSCE, index = NULL, bool = NULL, rowData = NULL, returnAsAltExp = TRUE, altExpName = "subset", prependAltExpName = TRUE )
inSCE |
Input SingleCellExperiment object. |
index |
Integer vector. Vector of indicies indicating which rows
to keep. If |
bool |
Boolean vector. Vector of |
rowData |
Character. An expression that will identify a subset of rows
using variables found in the |
returnAsAltExp |
Boolean. If |
altExpName |
Character. Name of the alternative experiment object to
add if |
prependAltExpName |
Boolean. If |
A SingleCellExperiment object that has been subsetted by rowData.
Joshua D. Campbell
data(scExample) # Set a variable up in the rowData indicating mitochondrial genes rowData(sce)$isMito <- ifelse(grepl("^MT-", rowData(sce)$feature_name), "yes", "no") sce <- subsetSCERows(sce, rowData = "isMito == 'yes'")