readTranscriptFeatures {genomation} | R Documentation

## Function for reading exon intron and promoter structure from a given bed file

### Description

Function for reading exon intron and promoter structure from a given bed file

### Usage

    readTranscriptFeatures(location,remove.unusual=TRUE,
                                  up.flank=1000,down.flank=1000,unique.prom=TRUE)

    ## S4 method for signature 'character'
    readTranscriptFeatures(location, remove.unusual = TRUE,
      up.flank = 1000, down.flank = 1000, unique.prom = TRUE)

### Arguments

`location` | location of the bed file with 12 or more columns. The file can end in `.gz`, `.bz2`, `.xz`, or `.zip` and/or start with `http://` or `ftp://`. If the file is not compressed it can also start with `https://` or `ftps://`.
`remove.unusual` | remove the chromomesomes with unsual names, mainly random chromsomes etc
`up.flank` | up-stream from TSS to detect promoter boundaries
`down.flank` | down-stream from TSS to detect promoter boundaries
`unique.prom` | get only the unique promoters, promoter boundaries will not have a gene name if you set this option to be TRUE

### Value

a `GRangesList` containing locations of exon/intron/promoter/TSS

### Note

one bed track per file is only accepted, the bed files with multiple tracks will cause en error

### Examples

    my.bed12.file = system.file("extdata/chr21.refseq.hg19.bed", package = "genomation")
    my.bed12.file
    feats = readTranscriptFeatures(my.bed12.file)
    names(feats)
    sapply(feats, head)

[Package genomation version 1.12.0 Index]