simple_filter: Filter genes with low expression

In Sage-Bionetworks/sageseqr: Identify differentially expressed genes counts data

Filter genes with low expression

Description

'simple_filter' converts a gene counts matrix into counts per million (CPM) and identifies the genes that meet the minimum CPM threshold in a percentage of samples. The minimum CPM threshold and percent threshold is user defined. The function returns a list of genes.

Usage

simple_filter(count_df, cpm_threshold, conditions_threshold)

Arguments

count_df	A counts data frame with sample identifiers as column names and gene Ids are rownames.
cpm_threshold	The minimum number of CPM allowed.
conditions_threshold	Percentage of samples that should contain the minimum CPM.

Examples

## Not run: 
gene_list <- simple_filter(count_df = counts, cpm_threshold = 1, condition_threshold = 0.5)

## End(Not run)

Sage-Bionetworks/sageseqr documentation built on June 13, 2024, 2:11 p.m.