filter_cells: Filter cells with quality control criteria

Description Usage Arguments Details Value Examples

View source: R/utils.R

Description

Remove low quality cell entries from object

Usage

1
2
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

1
2
3
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)

hjunwoo/ccfindR documentation built on Oct. 4, 2019, 10:31 a.m.