removeMissingObs {rliger} | R Documentation |
Remove cells/genes with no expression across any genes/cells
Description
Removes cells/genes from chosen slot with no expression in any genes or cells respectively.
Usage
removeMissingObs(
object,
slot.use = "raw.data",
use.cols = TRUE,
verbose = TRUE
)
Arguments
object |
|
slot.use |
The data slot to filter (takes "raw.data" and "scale.data") (default "raw.data"). |
use.cols |
Treat each column as a cell (default TRUE). |
verbose |
Print messages (TRUE by default) |
Value
liger
object with modified raw.data (or chosen slot) (dataset names preserved).
Examples
ligerex <- createLiger(list(ctrl = ctrl, stim = stim))
if (any(rowSums(ctrl) == 0) || any(rowSums(stim) == 0)) {
# example datasets do not have missing data, thus put in a condition
# Though the function will return unchanged object if no missing found
ligerex <- removeMissingObs(ligerex)
}
[Package rliger version 1.0.1 Index]