filter_cells: Filter cells with quality control criteria

In ccfindR: Cancer Clone Finder

Description

Remove low quality cell entries from object

Usage

filter_cells(object, umi.min = 0, umi.max = Inf, plot = TRUE,
  remove.zeros = TRUE)

Arguments

object	scNMFSet object
umi.min	Minimum UMI count for cell filtering
umi.max	Maximum UMI count for cell filtering
plot	If TRUE, the UMI count distribution of all cells will be displayed. Cells selected are colored red.
remove.zeros	Remove rows/columns containing zeros only

Details

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.

Value

scNMFSet object with cells filtered.

Examples

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)

ccfindR documentation built on Nov. 8, 2020, 5:12 p.m.