estimateSizeFactorsForMatrix: Low-level function to estimate size factors with robust...

In ABSSeq: ABSSeq: a new RNA-Seq analysis method based on modelling absolute expression differences

Description

This function is borrowed from DESeq.

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.

Details

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, you will not call this function directly.

Value

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

Author(s)

Simon Anders

References

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

Examples

data(simuN5)
dat <- simuN5
estimateSizeFactorsForMatrix(dat$counts)

ABSSeq documentation built on Nov. 8, 2020, 5:07 p.m.