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

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) )

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(DESeq)
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, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, 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, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

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'.
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/DESeq/estimateSizeFactorsForMatrix.Rd_%03d_medium.png", width=480, height=480)
> ### Name: estimateSizeFactorsForMatrix
> ### Title: Low-level function to estimate size factors with robust
> ###   regression.
> ### Aliases: estimateSizeFactorsForMatrix
> 
> ### ** Examples
> 
> cds <- makeExampleCountDataSet()
> estimateSizeFactorsForMatrix( counts(cds) )
       A1        A2        B1        B2        B3 
0.9636365 1.2592442 0.6772235 0.8772507 1.5528371 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>