computeVmat {VplotR} | R Documentation

## A function to compute Vplot matrix

### 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)]

[Package VplotR version 1.4.0 Index]