readBed {CNEr} | R Documentation

## Read bed file

### Description

Read the coordinates information from a bed file.

### Usage

      readBed(bedFile, assemblyFn=NULL)

### Arguments

`bedFile` | `character`(1): filename of the ‘bed’ file to read.
`assemblyFn` | `character`(1): filename of the twoBit or fasta file of the genome.

### Details

This function is designed to read the bed file as ‘chrom’, ‘chromStart’, ‘chromEnd’. The strand information is also stored where available.

In the bed file, the ‘chromStart’ is on the 0-based coordinate system while ‘chromEnd’ is on the 1-based coordinate system. For example, the first 100 bases of a chromosome are defined as ‘chromStart=0’, ‘chromEnd=100’, and span the bases numbered 0-99. When it is read into `GRanges`, both the ‘chromStart’ and ‘chromEnd’ are on 1-based coordinate, i.e., ‘chromStart=1’ and ‘chromEnd=100’.

When ‘assemblyFn’ is not `NULL`, the corresponding `Seqinfo` will be added into the returned `GRanges`.

### Value

A `GRanges` object is returned. When no strand information is available in the bed file, all the ranges are assumed to be on the positive strand.

### Author(s)

Ge Tan

### References

https://genome.ucsc.edu/FAQ/FAQformat.html#format1

### See Also

`import.bed`

### Examples

      bedFn <- file.path(system.file("extdata", package="CNEr"),
                         "filter_regions.hg38.bed")
      assemblyFn <- file.path(system.file("extdata",
                              package="BSgenome.Hsapiens.UCSC.hg38"),
                              "single_sequences.2bit")
      bed <- readBed(bedFn, assemblyFn=assemblyFn)

[Package CNEr version 1.22.0 Index]