importPEBamFiles {VplotR} | R Documentation

## A function to import paired end bam files as GRanges

### Description

This function takes bam file paths and read them into GRanges objects. Note: Can be quite lengthy for .bam files with 5+ millions fragments.

### Usage

    importPEBamFiles(
      files,
      genome = NULL,
      where = NULL,
      max_insert_size = 1000,
      shift_ATAC_fragments = FALSE,
      cores = 10,
      verbose = TRUE
    )

### Arguments

`files` | character vector, each element of the vector is the path of an individual .bam file.
`genome` | character, genome ID (e.g. sacCer3, ce11, dm6, danRer10, mm10 or hg38).
`where` | GRanges, only import the fragments mapping to the input GRanges (can fasten the import process a lot).
`max_insert_size` | Integer, filter out fragments larger than this size.
`shift_ATAC_fragments` | Boolean, if the fragments come from ATAC-seq, one might want to shift the extremities by +5 / -4 bp.
`cores` | Integer, number of cores to use when indexing bam files
`verbose` | Boolean

### Value

A GRanges object containing fragments from the input .bam file.

### Examples

    bamfile <- system.file("extdata", "ex1.bam", package = "Rsamtools")
    fragments <- importPEBamFiles(
        bamfile,
        shift_ATAC_fragments = TRUE
    )
    fragments

[Package VplotR version 1.4.0 Index]