computeVmat: A function to compute Vplot matrix

In VplotR: Set of tools to make V-plots and compute footprint profiles

Description

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.

Usage

computeVmat(
  bam_granges,
  granges,
  cores = 1,
  xlims = c(-250, 250),
  ylims = c(50, 300)
)

Arguments

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

Value

A table object

Examples

data(bam_test)
data(ce11_all_REs)
Vmat <- computeVmat(bam_test, ce11_all_REs)
dim(Vmat)
Vmat[seq(1,5), seq(1,10)]

VplotR documentation built on Nov. 8, 2020, 7:50 p.m.