qsva: A function for computing quality surrogate variables (qSVs)

In steveneschrich/msva: Surrogate Variable Analysis

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)

steveneschrich/msva documentation built on Dec. 23, 2021, 5:33 a.m.