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

In DESeq: Differential gene expression analysis based on the negative binomial distribution

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, [e-mail]

See Also

estimateSizeFactors

Examples

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

Example output

Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Loading required package: lattice
    Welcome to 'DESeq'. For improved performance, usability and
    functionality, please consider migrating to 'DESeq2'.
       A1        A2        B1        B2        B3 
0.9707209 1.2597721 0.6729935 0.8649272 1.5528209 

DESeq documentation built on April 28, 2020, 6:37 p.m.