getBaseMeansAndVariances {DESeq}R Documentation

Perform row-wise estimates of base-level means and variances for count data.

Description

This function is called internally by a number of other functions. You will need to call it directly only in very special cases.

Usage

getBaseMeansAndVariances(counts, sizeFactors)

Arguments

counts

a matrix of data frame of count data. All the columns of this matrix will be considered as replicates of the same condition.

sizeFactors

the size factors of the columns, as estimated e.g. with estimateSizeFactorsForMatrix

Details

This function is kept for backwards compatibility. See the example below for an alternative and more self-explanatory way to get the same data.

Value

A data frame with one row for each row in 'counts' and two columns:

baseMean

The base mean for each row. This is the mean of the counts after they have been divided by the size factors

comp2

The base variance for each row. This is the variance of the counts after they have been divided by the size factors

Author(s)

Simon Anders, sanders@fs.tum.de

Examples

cds <- makeExampleCountDataSet()
cds <- estimateSizeFactors( cds )
head( getBaseMeansAndVariances( counts(cds), sizeFactors(cds) ) )

# You can get the same as follows
head( rowMeans( counts( cds, normalized=TRUE ) ) )
head( genefilter::rowVars( counts( cds, normalized=TRUE ) ) )

[Package DESeq version 1.6.1 Index]