estimateSizeFactorsForMatrix
From DESeq2 v1.12.3
by Michael Love
Lowlevel function to estimate size factors with robust regression.
Given a matrix or data frame of count data, this function estimates the size
factors as follows: Each column is divided by the geometric means of the
rows. The median (or, if requested, another location estimator) of these
ratios (skipping the genes with a geometric mean of zero) is used as the size
factor for this column. Typically, one will not call this function directly, but use
estimateSizeFactors
.
Usage
estimateSizeFactorsForMatrix(counts, locfunc = stats::median, geoMeans, controlGenes)
Arguments
 counts
 a matrix or data frame of counts, i.e., nonnegative integer values
 locfunc
 a function to compute a location for a sample. By default, the
median is used. However, especially for low counts, the
shorth
function from genefilter may give better results.  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
 controlGenes
 optional, numeric or logical index vector specifying those genes to use for size factor estimation (e.g. housekeeping or spikein genes)
Value

a vector with the estimates size factors, one element per column
See Also
Examples
dds < makeExampleDESeqDataSet()
estimateSizeFactorsForMatrix(counts(dds))
geoMeans < exp(rowMeans(log(counts(dds))))
estimateSizeFactorsForMatrix(counts(dds),geoMeans=geoMeans)
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