sizeFactors: Accessor functions for the 'sizeFactors' information in a...

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

Description

The sizeFactors vector assigns to each column of the count data a value, the size factor, such that count values in the columns can be brought to a common scale by dividing by the corresponding size factor.

Usage

## S4 method for signature 'CountDataSet'
sizeFactors(object)
## S4 replacement method for signature 'CountDataSet,numeric'
sizeFactors(object) <- value

Arguments

object	a CountDataSet object.
value	a numeric vector, one size factor for each column in the count data.

Author(s)

Simon Anders, [e-mail]

See Also

estimateSizeFactors

Examples

   cds <- makeExampleCountDataSet()
   cds <- estimateSizeFactors( cds )
   sizeFactors(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 
0.9619461 1.2557122 0.6854428 0.8682402 1.5627566 

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