defIgRanges: Define intergenic genomic regions

In pram: Pooling RNA-seq datasets for assembling transcript models

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')

pram documentation built on Nov. 8, 2020, 11:08 p.m.