read.degradation.matrix {sva} | R Documentation |
This function reads in degradation regions to form a library-size- and read-length-normalized degradation matrix for subsequent RNA quality correction
read.degradation.matrix(covFiles, sampleNames, totalMapped, readLength = 100, normFactor = 8e+07, type = c("bwtool", "region_matrix_single", "region_matrix_all"), BPPARAM = bpparam())
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 |
the normalized degradation matrix, region by sample
# 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)