GTF-class: Reference class to manipulate GTF data

In jokergoo/GTF: GTF class

Description

Reference class to manipulate GTF data

Fields

GTF

complicated structure of list

sorted

data is sorted or not

Methods

geneLength(type = c("gene", "exon"))

get gene/exon length

getGeneID(index = NULL)

get Gene ID (ensembl ID)

getTranscriptsByGeneID(geneID)

get transcripts by gene IDs

getValueByGeneID(geneID, type = c("chr", "name", "strand", "type", "end", "start"))

get values corresponding to gene IDs

mergeTranscripts(mc.cores = 1)

merge alternative transcripts into one union gene

read(gtf)

read from GTF file

sort()

sort GTF

toBed(file = NULL, type = c("gene", "exon"), chromosome = paste("chr", c(1:22, "X", "Y"), sep = ""))

convert and write to BED file

write(file)

write to GTF file

Examples

## Not run: 
library(GTF)
gencode = new("GTF")
gencode$read(paste(system.file(package = "GTF"), "/extdata/test.gtf", sep=""))
gencode$mergeTranscripts()
gencode$mergeTranscripts(mc.cores = 2)
gencode$write("output.gtf")
gene_length = gencode$geneLength("exon")
gene = gencode$toBed(type = "gene")
exon = gencode$toBed(type = "exon")
gencode$toBed(file = "gene.bed", type = "gene")
gencode$toBed(file = "exon.bed", type = "exon")
gi = gencode$getGeneID(1:10)
chr = gencode$getValueByGeneID(gi, type = "chr")
tr = gencode$getTranscriptsByGeneID(gi)

## End(Not run)

jokergoo/GTF documentation built on May 19, 2019, 6:23 p.m.