getNormFactors {icetea} | R Documentation

## Calculate normalization factors from CapSet object

### 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")

[Package icetea version 1.8.0 Index]