bedToGRangesList {preciseTAD} | R Documentation

## Function to create a GRangesList object from functional genomic annotation data in the form of BED files

### Description

Function to create a GRangesList object from functional genomic annotation data in the form of BED files

### Usage

    bedToGRangesList(
      filepath,
      bedList = NULL,
      bedNames = NULL,
      pattern = "*.bed",
      signal = NULL
    )

### Arguments

`filepath` | Character describing the path to the folder containing the BED files of functional genomic annotations. This is ignored if bedList is specified.
`bedList` | A list object containing the bed data as data frames to be converted into a GRangesList. The data frames must include at least chromosome, start, and end coordinates as the first 3 columns. Default is NULL.
`bedNames` | A character vector to provide names to the GRangesList, should be in the order of bedList. Default is NULL.
`pattern` | Character describing the pattern of the files for the functional genomic annotations. Default is "*.bed".
`signal` | The column number in the BED files that denotes coverage strength. Must be the same for all files. Default is NULL indicating to no coverage value is to be used.

### Value

A `GRangesList` object where each entry is a `GRanges` object specific to each BED file in the path provided

### Examples

    #set path
    path <- system.file("extdata", package = "preciseTAD")
    #contains 2 BED files representing YY1 and NFYA
    #transcription factor binding sites for GM12878
    tfbsList <- bedToGRangesList(filepath = path, bedList=NULL, bedNames=NULL,
    pattern = "*.bed", signal=NULL)

[Package preciseTAD version 1.2.0 Index]