filter_cells {ccfindR} | R Documentation |
Remove low quality cell entries from object
filter_cells(object, umi.min = 0, umi.max = Inf, plot = TRUE, remove.zeros = TRUE)
object |
|
umi.min |
Minimum UMI count for cell filtering |
umi.max |
Maximum UMI count for cell filtering |
plot |
If |
remove.zeros |
Remove rows/columns containing zeros only |
Takes as input scNMFSet
object and plots histogram of UMI
counts for each
cell. Optionally, cells are filtered using minimum and maximum UMI counts.
The resulting object is returned after removing empty rows and columns,
if any.
scNMFSet
object with cells filtered.
set.seed(1) s <- scNMFSet(matrix(stats::rpois(n=1200,lambda=3),40,30)) s <- filter_cells(s,umi.min=10^2.0,umi.max=10^2.1)