estimateGeneDispersion: Estimates gene-specific dispersion estimates for total and...

In carinademel/RNAlife: Quantifying kinetic parameters to determine the RNA life cycle

Description

Estimates gene-specific dispersion estimates for total and labeled samples, using DESeq2 The DESeq estimation does only work correctly, if at least two samples are available for each class(labeled/total), either replicates or different conditions.

Usage

estimateGeneDispersion(counts, conditions.labeling,
  conditions = colnames(counts), type = c("dispersion", "dispGeneEst",
  "dispFit", "dispMAP"))

Arguments

counts	count table for genes (rows) and samples (columns)
conditions.labeling	vector indicating for each sample if it was labeled ("L") or total ("T")
conditions	vector giving the experimental condition for each sample
type	type of disperion from deseq, "dispersion"=="dispMAP"

Value

data.frame with dispersion estimates for every gene (rows) and labeled and total samples(columns)

Author(s)

Carina Demel

Examples

data(gene.counts)
data(samples)
dispersion = estimateGeneDispersion(gene.counts, samples$conditions.labeling, samples$conditions)

carinademel/RNAlife documentation built on May 13, 2019, 12:43 p.m.