estimateSizeFactorsForMatrix {DESeq2} | R Documentation

## 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

### See Also

`estimateSizeFactors`

### Examples

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

[Package DESeq2 version 1.32.0 Index]