getNormFactors: Calculate normalization factors from CapSet object

In vivekbhr/icetea: Integrating Cap Enrichment with Transcript Expression Analysis

Description

Calculate normalization factors from CapSet object

Usage

getNormFactors(CSobject, features, method = "TMM", ...)

## S4 method for signature 'CapSet'
getNormFactors(CSobject, features, method = "TMM", ...)

Arguments

CSobject	An object of class CapSet
features	A GRanges-class.object to count the reads on.
method	Method to use for normalization. Options : "TMM","RLE","upperquartile","none"
...	Additional arguments passed to calcNormFactors

Value

Numeric vector of calculated normalization factors.

Examples

 # load a txdb object
 library("TxDb.Dmelanogaster.UCSC.dm6.ensGene")
 seqlevelsStyle(TxDb.Dmelanogaster.UCSC.dm6.ensGene) <- "ENSEMBL"

 # get genes (only X chromsome, for simplicity)
 seqlevels(TxDb.Dmelanogaster.UCSC.dm6.ensGene) <- "X"
 dm6genes <- genes(TxDb.Dmelanogaster.UCSC.dm6.ensGene)

# get norm factors by counting reads on genes
cs <- exampleCSobject()
normfacs <- getNormFactors(cs, dm6genes, method = "RLE")

vivekbhr/icetea documentation built on June 8, 2020, 4:45 a.m.