estimateSizeFactors {DESeq2} | R Documentation |
Estimate the size factors for a DESeqDataSet
## S4 method for signature 'DESeqDataSet' estimateSizeFactors(object,locfunc=median,geoMeans) ## S4 method for signature 'DESeqDataSet' estimateSizeFactors(object, locfunc = median, geoMeans)
object |
a DESeqDataSet |
locfunc |
a function to compute a location for a
sample. By default, the median is used. However,
especially for low counts, the
|
geoMeans |
by default this is not provided and the geometric means of the counts are calculated within the function. A vector of geometric means from another count matrix can be provided for a "frozen" size factor calculation |
This function estimates the size factors using the "median
ratio method" described by Equation 5 in Ander and Huber
(2010). The estimated size factors can be accessed using
sizeFactors
. Alternative library size
estimators can also be supplied using
sizeFactors
.
Typically, the function is called with the idiom:
dds <- estimateSizeFactors(dds)
See DESeq
for a description of the use of
size factors in the GLM. You need to call this function
after DESeqDataSet
unless you have manually
specified sizeFactors
. Alternatively,
gene-specific normalization factors for each sample can be
provided using normalizationFactors
which
will always preempt sizeFactors
in
calculations.
Internally, the function calls
estimateSizeFactorsForMatrix
, which provides
more details on the calculation.
The DESeqDataSet passed as parameters, with the size factors filled in.
Simon Anders
Simon Anders, Wolfgang Huber: Differential expression analysis for sequence count data. Genome Biology 11 (2010) R106, http://dx.doi.org/10.1186/gb-2010-11-10-r106
dds <- makeExampleDESeqDataSet() dds <- estimateSizeFactors(dds) sizeFactors(dds) geoMeans <- exp(rowMeans(log(counts(dds)))) dds <- estimateSizeFactors(dds,geoMeans=geoMeans) sizeFactors(dds)