min_filter_counts: Filter low-count genes

In mjdufort/countSubsetNorm: RNAseq counts subsetting and normalizing.

Description

This function filters a counts object, removing genes that do not meet a minimum count value in a minimum percentage of libraries

Usage

min_filter_counts(counts, min_count=NULL, min_cpm=NULL, min_libs_perc=0.15)

Arguments

counts	a matrix or data frame of gene expression counts; should have samples in columns and genes in rows.
min_count	numeric value, the minimum count value. Either this or min_cpm should be specified, but not both.
min_cpm	numeric values, the minimum counts per million value. Either this or min_cpm should be specified, but not both.
min_libs_perc	numeric value, the minimum percentage of libraries with counts or cpm equal to or greater than the threshold.

Details

Genes are removed from counts if they do not have at least min_count counts in at least min_libs_perc Note that adding or removing libraries to/from the counts object may change the genes that meet these thresholds.

Value

a filtered matrix or data frame with the same number of columns as counts, and potentially fewer rows. Counts are retained in the units they are input (using min_cpm does not convert counts to cpm).

mjdufort/countSubsetNorm documentation built on Nov. 7, 2019, 6:37 p.m.