qAbundanceDist: Gene abundance proportion distribution of RNA-seq data.

In tcgsaseq: Time-Course Gene Set Analysis for RNA-Seq Data

Description

An example of gene abundance proportion distribution function of RNA-seq data, generated from a real dataset. See supplementary material of Law et al.

Usage

data(qAbundanceDist)

Format

A function: qAbundanceDist.

Source

http://bioinf.wehi.edu.au/voom/

References

Law CW, Chen Y, Shi W & Smyth GK, voom: Precision weights unlock linear model analysis tools for RNA-seq read counts, Genome Biology, 15(2), R29, 2014.

Examples

## Not run: 
# Get distribution function of abundance proportions
# This distribution was generated from a real dataset
#load(url("http://bioinf.wehi.edu.au/voom/qAbundanceDist.RData"))
data("qAbundanceDist")
curve(qAbundanceDist, from=0, to =0.99)

# Generate baseline proportions for desired number of genes
ngenes <- 10000
baselineprop <- qAbundanceDist( (1:ngenes)/(ngenes+1) )
baselineprop <- baselineprop/sum(baselineprop)

## End(Not run)

tcgsaseq documentation built on Sept. 13, 2020, 5:13 p.m.