defIgRanges {pram} | R Documentation

## Define intergenic genomic regions

### Description

Define intergenic genomic regions

### Usage

    defIgRanges(in_gtf, chromgrs, genome = NULL, fchromsize = NULL,
        radius = 10000, feat = "exon", chroms = NULL)

### Arguments

`in_gtf` | An input GTF file for defining genomic coordinates of existing genes. Required to have 'gene_id' in the attribute column (column 9)
`chromgrs` | A GRanges object defining chromosome sizes.
`genome` | Version of the genome. Will be used when 'chromgrs' is missing. Currently supported ones are: hg19 hg38 mm9 mm10 All the above genomes have sizes for all chromosomes including random and alt ones. Default: NULL
`fchromsize` | Name of a file defining chromosome sizes. Will be used when 'chromgrs' and 'genome' are missing. It can be downloaded from UCSC, e.g. for hg19, http://hgdownload.cse.ucsc.edu/ goldenpath/hg19/database/chromInfo.txt.gz Required to have at least two tab-delimited columns without any header: chromosome name, e.g. chr1 chromosome length, e.g. 249250621 Both uncompressed and gzipped files are supported. Default: NULL
`radius` | Region length (bp) of gene's upstream and downstream to be excluded from intergenic region. Default: 10,000
`feat` | Feature in the GTF file (column 3) to-be-used for defining genic region. Default: exon
`chroms` | A vector of chromosomes names to define intergenic regions. e.g. c('chr10', 'chr11') Default: NULL

### Value

a GRanges object of intergenic regions

### Examples

    fgtf = system.file('extdata/gtf/defIgRanges_in.gtf', package='pram')

    defIgRanges(fgtf, genome='hg38')

[Package pram version 1.4.0 Index]