getFragmentsDistribution {VplotR} | R Documentation

## A function to compute sizes distribution for paired-end fragments

### Description

This function takes fragments and compute the distribution of their sizes over a set or multiple sets of GRanges.

### Usage

    getFragmentsDistribution(
      fragments,
      granges_list = NULL,
      extend_granges = c(-500, 500),
      limits = c(0, 600),
      roll = 3,
      cores = 1
    )

### Arguments

`fragments` | GRanges object containing paired-end fragments. See importPEBamFiles for more details on how to create such object.
`granges_list` | GRanges, can be a list of different sets of GRanges.
`extend_granges` | numeric vector of length 2, how the GRanges should be extended.
`limits` | numeric vector of length 2, only consider fragments within this window of sizes.
`roll` | Integer, apply a moving average of this size
`cores` | Integer, number of threads used to compute fragment size distribution

### Value

A list of tbl, one for each .bam file.

### Examples

    data(bam_test)
    data(ce11_proms)
    df <- getFragmentsDistribution(
        bam_test,
        ce11_proms,
        extend_granges = c(-500, 500)
    )
    head(df)
    which.max(df$y)

[Package VplotR version 1.4.0 Index]