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 )