downsample.counts: Downsample read counts

In metaseqR: An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms.

Description

This function downsamples the library sizes of a read counts table to the lowest library size, according to the methdology used in (Soneson and Delorenzi, BMC Bioinformatics, 2013).

Usage

    downsample.counts(counts,seed=42)

Arguments

counts	the read counts table which is subjected to downsampling.
seed	random seed for reproducible downsampling.

Value

The downsampled counts matrix.

Author(s)

Panagiotis Moulos

Examples

## Dowload locally the file "bottomly_count_table.txt" from
## the ReCount database
#download.file(paste("http://bowtie-bio.sourceforge.net/",
#    "recount/countTables/bottomly_count_table.txt",sep=""),
#    destfile="~/bottomly_count_table.txt")
#M <- as.matrix(read.delim("~/bottomly_count_table.txt",row.names=1))
#D <- downsample.counts(M)

metaseqR documentation built on Nov. 8, 2020, 5:57 p.m.