DESeq2: estimateSizeFactorsForMatrix – R documentation

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estimateSizeFactorsForMatrix

Low-level function to estimate size factors with robust regression.

Description

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,
  type = c("ratio", "poscounts")
)

Arguments

`counts`	a matrix or data frame of counts, i.e., non-negative 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 spike-in genes)
`type`	standard median ratio (`"ratio"`) or where the geometric mean is only calculated over positive counts per row (`"poscounts"`)

Value

a vector with the estimates size factors, one element per column

Author(s)

Simon Anders

Examples

dds <- makeExampleDESeqDataSet()
estimateSizeFactorsForMatrix(counts(dds))
geoMeans <- exp(rowMeans(log(counts(dds))))
estimateSizeFactorsForMatrix(counts(dds),geoMeans=geoMeans)

DESeq2

Differential gene expression analysis based on the negative binomial distribution

v1.30.1

LGPL (>= 3)

Authors

Michael Love [aut, cre], Constantin Ahlmann-Eltze [ctb], Kwame Forbes [ctb], Simon Anders [aut, ctb], Wolfgang Huber [aut, ctb]

Initial release