filter_low_var: Filtering genes with low variability

In Kumquatum/GWENA: Pipeline for augmented co-expression analysis

Filtering genes with low variability

Description

Remove low variating genes based on the percentage given and the type of variation specified.

Usage

filter_low_var(data_expr, pct = 0.8, type = c("mean", "median", "mad"))

Arguments

data_expr	matrix or data.frame or SummarizedExperiment, table of expression values (either microarray or RNA-seq), with genes as column and samples as row
pct	float, percentage of gene to keep, value must be in ]0;1[
type	string, function name used for filtration. Should be either "mean", "median", or "mad"

Value

A data.frame of filtered genes

Examples

df <- matrix(abs(rnorm(15*45)), 15)
colnames(df) <- paste0("gene_", seq_len(ncol(df)))
rownames(df) <- paste0("sample_", seq_len(nrow(df)))
df_filtered <- filter_low_var(df)

Kumquatum/GWENA documentation built on July 7, 2023, 3:41 p.m.