filterByCPM.matrix: Filter lowly expressed genes by CPM

In bedapub/ribiosNGS: Utilities for next-generation sequencing data analysis in ribios

Filter lowly expressed genes by CPM

Description

Filter lowly expressed genes by CPM

Usage

## S3 method for class 'matrix'
filterByCPM(obj, minCPM = 1, minCount = 1, ...)

Arguments

obj	A matrix
minCPM	Numeric, the minimum CPM accepted as expressed in one sample
minCount	Integer, how many samples must have CPM larger than minCPM to keep this gene?
...	Not used

Value

A logical vector of the same length as the row count of the matrix. TRUE means the gene is reasonably expressed, and FALSE means the gene is lowly expressed and should be filtered (removed)

Examples

set.seed(1887)
mat <- rbind(matrix(rbinom(125, 5, 0.25), nrow=25), rep(0, 5))
filterByCPM(mat)

bedapub/ribiosNGS documentation built on Feb. 10, 2025, 12:34 a.m.