computeVmat {VplotR} | R Documentation |
This function computes the underlying matrix shown as a heatmap in Vplots. For each pair of coordinates (x: distance from fragment midpoint to center of GRanges of interest; y: fragment size), the function computes how many fragments there are.
computeVmat( bam_granges, granges, cores = 1, xlims = c(-250, 250), ylims = c(50, 300) )
bam_granges |
GRanges, paired-end fragments |
granges |
GRanges, regions to map the fragments onto |
cores |
Integer, nb of threads to parallelize fragments subsetting |
xlims |
The x limits of the computed Vmat |
ylims |
The y limits of the computed Vmat |
A table object
data(bam_test) data(ce11_all_REs) Vmat <- computeVmat(bam_test, ce11_all_REs) dim(Vmat) Vmat[seq(1,5), seq(1,10)]