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
)
Input SingleCellExperiment object.
Integer vector. Vector of indicies indicating which rows
to keep. If NULL
, this will not be used for subsetting.
Default NULL
.
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
.
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
.
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.
Character. Name of the alternative experiment object to
add if returnAsAltExp = TRUE
. Default subset
.
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
.
A SingleCellExperiment object that has been subsetted by rowData.