plotVmat.GRanges {VplotR} | R Documentation |
The plotVmat.GRanges() method computes and normalizes a Vmat before passing it to plotVmat.Vmat() method.
## S3 method for class 'GRanges' plotVmat( x, granges, xlims = c(-250, 250), ylims = c(50, 300), normFun = "", s = 0.95, roll = 3, cores = 1, return_Vmat = FALSE, verbose = 1, ... )
x |
GRanges, paired-end fragments |
granges |
GRanges, loci to map the fragments onto |
xlims |
x limits of the computed Vmat |
ylims |
y limits of the computed Vmat |
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. |
cores |
Integer, number of threads to parallelize fragments subsetting |
return_Vmat |
Boolean, should the function return the computed Vmat rather than the plot? |
verbose |
Boolean |
... |
additional parameters |
A Vmat ggplot
data(bam_test) data(ce11_proms) V <- plotVmat( bam_test, ce11_proms, normFun = 'libdepth+nloci', roll = 5 )