normalizeVmat {VplotR} | R Documentation |
This function normalizes a Vmat. Several different approaches have been implemented to normalize the Vmats.
normalizeVmat( Vmat, bam_granges, granges, normFun = c("zscore"), s = 0.99, roll = 1, verbose = TRUE )
Vmat |
A Vmat, usually output of computeVmat |
bam_granges |
GRanges, the paired-end fragments |
granges |
GRanges, the regions to map the fragments onto |
normFun |
character. A Vmat should be scaled either by:
|
s |
A float indicating which quantile to use if 'quantile' normalization is chosen |
roll |
integer, to use as the window to smooth the Vmat rows by rolling mean. |
verbose |
Boolean |
A normalized Vmat object
data(bam_test) data(ce11_all_REs) Vmat <- computeVmat(bam_test, ce11_all_REs) Vmat <- normalizeVmat( Vmat, bam_test, ce11_all_REs, normFun = c('libdepth+nloci') )