read.degradation.matrix: A function for reading in coverage data from...

In steveneschrich/msva: Surrogate Variable Analysis

Description

This function reads in degradation regions to form a library-size- and read-length-normalized degradation matrix for subsequent RNA quality correction

Usage

read.degradation.matrix(
  covFiles,
  sampleNames,
  totalMapped,
  readLength = 100,
  normFactor = 8e+07,
  type = c("bwtool", "region_matrix_single", "region_matrix_all"),
  BPPARAM = bpparam()
)

Arguments

covFiles	coverage file(s) for degradation regions
sampleNames	sample names; creates column names of degradation matrix
totalMapped	how many reads per sample (library size normalization)
readLength	read length in base pairs (read length normalization)
normFactor	common library size to normalize to; 80M reads as default
type	whether input are individual 'bwtool' output, 'region_matrix' run on individual samples, or 'region_matrix' run on all samples together
BPPARAM	(Optional) BiocParallelParam for parallel operation

Value

the normalized degradation matrix, region by sample

Examples

# bwtool
bwPath = system.file('extdata', 'bwtool', package = 'sva')
degCovAdj = read.degradation.matrix(
 covFiles = list.files(bwPath,full.names=TRUE),
 sampleNames = list.files(bwPath), readLength = 76, 
 totalMapped = rep(100e6,5),type="bwtool")
 head(degCovAdj)
 
# region_matrix: each sample
r1Path = system.file('extdata', 'region_matrix_one', package = 'sva')
degCovAdj1 = read.degradation.matrix(
 covFiles = list.files(r1Path,full.names=TRUE),
 sampleNames = list.files(r1Path), readLength = 76, 
 totalMapped = rep(100e6,5),type="region_matrix_single")
 head(degCovAdj1)
 
r2Path = system.file('extdata', 'region_matrix_all', package = 'sva')
degCovAdj2 = read.degradation.matrix(
 covFiles = list.files(r2Path,full.names=TRUE),
 sampleNames = list.files(r1Path), readLength = 76, 
 totalMapped = rep(100e6,5),type="region_matrix_all")
head(degCovAdj2)

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