Filter genes with low expression

Source: R/functions.R

`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.

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

if (FALSE) {
gene_list <- simple_filter(count_df = counts, cpm_threshold = 1, condition_threshold = 0.5)
}