extractCounts {RaceID} | R Documentation |
Description
This function discards lowly expressed genes from a count matrix stored in an SCseq
object, and returns (normalized or non-normalized) gene expression or noise values.
Usage
extractCounts(
object,
minexpr = 5,
minnumber = 5,
noise = FALSE,
pt = NULL,
n = NULL,
g = NULL,
norm = TRUE
)
Arguments
|
SCseq class object.
|
|
Integer number greater or equal to zero. Minimum expression of a gene in at least minnumber cells to not be discarded. Default is 5.
|
|
Integer number greater or equal to zero. Minimum number of cells required to have at least minexpr transcript counts for a gene to not be discarded. Default is 5.
|
|
logical. If TRUE , then noise (in object@noise ) is returned for the filtered genes and cells. Default is FALSE and gene expression counts are returned.
|
|
List object returned by function pseudoTime . If given, then feature matrix is returned for cells in pt$ord and ordered by pseudo-time. Default is NULL and feature matrix is returned for all cells in object$ndata .
|
|
Vector of valid column names corresponding to a subset of valid column names of the object@ndata . Default is NULL filtering is done on all cells in object@ndata . Only considered if pt is NULL.
|
|
Vector of gene IDs (valid row names of object@ndata ). If given, then all genes not in g are discarded prior to filtering. Default is NULL and filtering is done on all genes in object@ndata .
|
|
logical. If TRUE , then transcipt counts are normalized to the minimum number of total transcript counts across all cells in the feature matrix.
|
Value
Filtered expression matrix.
[Package
RaceID version 0.3.7
Index]