Calculate normalization factors from CapSet object

Source: R/AllGenerics.R, R/detectDiffTSS.R

Calculate normalization factors from CapSet object

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

# S4 method for 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()
#> Checking de-multiplexed R1 reads
#> Checking de-multiplexed R2 reads
#> Checking mapped file
#> Checking de-duplicated file
normfacs <- getNormFactors(cs, dm6genes, method = "RLE")