qsva {sva} | R Documentation |
This function computes quality surrogate variables (qSVs) from the library-size- and read-length-normalized degradation matrix for subsequent RNA quality correction
qsva(degradationMatrix, mod = matrix(1, ncol = 1, nrow = ncol(degradationMatrix)))
degradationMatrix |
the normalized degradation matrix, region by sample |
mod |
(Optional) statistical model used in DE analysis |
the qSV adjustment variables
## 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)