gtf_to_annotation: get annotation from GTF

In soulong/AnnotationHub: a hub for rapid loading annotation data and providing functions to reproduce annotation data

Description

extract tx2gene and gene annotation file from gtf file

Usage

gtf_to_annotation(gtf_file, species = "hs", datasource = "ensembl",
  server = "asia.ensembl.org", fp = c("EGFP", "mCherry", "tdTomato",
  "ZsGreen", "turboGFP", "mNeonGreen", "mScarleti"))

Arguments

gtf_file	a gtf file, typically downloaded from ensembl(http://www.ensembl.org/info/data/ftp/index.html)
species	it must be one of hs, mm
datasource	dataSrouce, like "ensembl GRCh38.95"
server	define a server which biomaRt will use
fp	if NULL, adding fp info will be omitted, if suppied with a vector(Default), then it will be added.

Value

a list with two items, tx2gene was used for conversion between transcript and gene, annotation was gene annotation info

Examples

gtf <- "~/Desktop/Mus_musculus.GRCm38.95.gtf"
grcm38 <- gtf_to_annotation(gtf, "mm", "ensembl_GRCm38.95") %>% .[[2]] %>% head()

soulong/AnnotationHub documentation built on July 6, 2019, 3:17 a.m.