GTF-class: Reference class to manipulate GTF data

Description Fields Methods Examples

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

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## 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 18, 2017, 5:15 a.m.