estimateSizeFactorsForMatrix {DESeq} | 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, ir 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, you will not call this function directly, but use `estimateSizeFactors`.

### Usage

    estimateSizeFactorsForMatrix( counts, locfunc=median)

### 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` may give better results.

### Value

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

### Author(s)

Simon Anders, sanders@fs.tum.de

### See Also

`estimateSizeFactors`

### Examples

    cds <- makeExampleCountDataSet()
    estimateSizeFactorsForMatrix( counts(cds) )

[Package DESeq version 1.39.0 Index]