hpgl_filter_counts: Filter low-count genes from a data set using cpm data and a...

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Filter low-count genes from a data set using cpm data and a threshold.

Description

This is identical to cbcb_filter_counts except it does not do the somewhat tortured log2CPM() but instead just uses a 4 cpm non-log threshold. It should therefore give basically the same result, but without the shenanigans.

Usage

hpgl_filter_counts(
  count_table,
  threshold = 2,
  min_samples = 2,
  libsize = NULL,
  ...
)

Arguments

count_table	Data frame of (pseudo)counts by sample.
threshold	Lower threshold of counts for each gene.
min_samples	Minimum number of samples.
libsize	Table of library sizes.
...	Arguments passed to cpm and friends.

Value

Dataframe of counts without the low-count genes.

See Also

[edgeR]

Examples

## Not run: 
 filtered_table <- cbcb_filter_counts(count_table)

## End(Not run)

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.