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.
Integer vector. Vector of indicies indicating which rows
to keep. If NULL, this will not be used for subsetting.
Default NULL.
bool
Boolean vector. Vector of TRUE or FALSE
indicating which rows should be kept. Needs to be the same length as the
number of rows in inSCE. If NULL, this will not be used
for subsetting. Default NULL.
rowData
Character. An expression that will identify a subset of rows
using variables found in the rowData of inSCE. For example,
if x is a numeric vector in rowData, then "x < 5" will
return all rows with x less than 5. Single quotes should be used for
character strings. For example, "y == 'yes'" will return all
rows where y is "yes". Multiple expressions can be evaluated by placing them
in a vector. For example c("x < 5", "y =='yes'") will apply both
operations for subsetting. If NULL, this will not be used for
subsetting. Default NULL.
returnAsAltExp
Boolean. If TRUE, the subsetted
SingleCellExperiment object will be returned in the
altExp slot of inSCE. If FALSE, the subsetted
SingleCellExperiment object will be directly returned.
altExpName
Character. Name of the alternative experiment object to
add if returnAsAltExp = TRUE. Default subset.
prependAltExpName
Boolean. If TRUE, altExpName will
be added to the beginning of the assay names in the altExp object.
This is only utilized if returnAsAltExp = TRUE. Default TRUE.
Value
A SingleCellExperiment object that has
been subsetted by rowData.
Author(s)
Joshua D. Campbell
Examples
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data(scExample)# Set a variable up in the rowData indicating mitochondrial genesrowData(sce)$isMito<-ifelse(grepl("^MT-",rowData(sce)$feature_name),"yes","no")sce<-subsetSCERows(sce,rowData="isMito == 'yes'")