sva: qsva – R documentation

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qsva

A function for computing quality surrogate variables (qSVs)

Description

This function computes quality surrogate variables (qSVs) from the library-size- and read-length-normalized degradation matrix for subsequent RNA quality correction

Usage

qsva(
  degradationMatrix,
  mod = matrix(1, ncol = 1, nrow = ncol(degradationMatrix))
)

Arguments

`degradationMatrix`	the normalized degradation matrix, region by sample
`mod`	(Optional) statistical model used in DE analysis

Value

the qSV adjustment variables

Examples

## Find files
bwPath <- system.file('extdata', 'bwtool', package = 'sva')

## Read the data
degCovAdj = read.degradation.matrix(
 covFiles = list.files(bwPath,full.names=TRUE),
 sampleNames = list.files(bwPath), readLength = 76, 
 totalMapped = rep(100e6,5),type="bwtool")

## Input data
 head(degCovAdj)

## Results
qsva(degCovAdj)

sva

Surrogate Variable Analysis

v3.38.0

Artistic-2.0

Authors

Jeffrey T. Leek <jtleek@gmail.com>, W. Evan Johnson <wej@bu.edu>, Hilary S. Parker <hiparker@jhsph.edu>, Elana J. Fertig <ejfertig@jhmi.edu>, Andrew E. Jaffe <ajaffe@jhsph.edu>, Yuqing Zhang <zhangyuqing.pkusms@gmail.com>, John D. Storey <jstorey@princeton.edu>, Leonardo Collado Torres <lcolladotor@gmail.com>

Initial release