| estimateSizeFactors {DESeq} | R Documentation |
Estimate the size factors for a CountDataSet
## S4 method for signature 'CountDataSet' estimateSizeFactors( object, locfunc=median, ... )
object |
a CountDataSet |
locfunc |
a function to compute a location for a sample. By default, the median is used. However,
especially for low counts, the |
... |
extra arguments are ignored |
You need to call this function right after newCountDataSet unless
you have manually specified size factors.
Typically, the function is called with the idiom
cds <- estimateSizeFactors( cds )
This estimates the size factors and stores the information in the object.
Internally, the function calls estimateSizeFactorsForMatrix. See there
for more details on the calculation.
The CountDataSet passed as parameters, with the size factors filled in.
Simon Anders, sanders@fs.tum.de
cds <- makeExampleCountDataSet() cds <- estimateSizeFactors( cds ) sizeFactors( cds )