count_filter: Filter RNA-seq expression table

In zshao1/ERSSA: Empirical RNA-seq Sample Size Analysis

Filter RNA-seq expression table

Description

count_filter function filters the RNA-seq count table to remove non- and low-expression genes at an defined average CPM cutoff (Default=1).

Usage

count_filter(count_table = NULL, cutoff = 1)

Arguments

count_table	A RNA-seq count matrix with genes on each row and samples on each column.
cutoff	Any gene with average CPM below this cutoff value will be filtered out.

Value

The filtered count table.

Author(s)

Zixuan Shao, [e-mail]

Examples

# load simple GTeX example count table
# example dataset containing 1000 genes, 4 replicates
data(count_table.partial, package = "ERSSA")

#filter the counts
count_table.filtered.partial = count_filter(count_table.partial)

zshao1/ERSSA documentation built on July 19, 2023, 9:20 p.m.