getNormFactors {icetea} | R Documentation |
Calculate normalization factors from CapSet object
getNormFactors(CSobject, features, method = "TMM", ...) ## S4 method for signature 'CapSet' getNormFactors(CSobject, features, method = "TMM", ...)
CSobject |
An object of class |
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 |
Numeric vector of calculated normalization factors.
# 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")