pharse_gtf: pharse annotation from local gtf file

In soulong/annoHub: A package for create and store enrichment analysis database

Description

prase txdb, gene annotation from local gtf file

Usage

pharse_gtf(
  gtf,
  species = "hs",
  geonme = "GRCh38",
  datasource = "Ensembl",
  version = "Ensembl v95",
  server = "asia.ensembl.org",
  fp = c("EGFP", "mCherry", "tdTomato", "ZsGreen", "turboGFP", "mNeonGreen",
    "mScarleti", "WPRE")
)

Arguments

gtf	character, file path to GTF file
species	character, one of hs, mm
geonme	character, genome build version like "GRCh38"
datasource	character, source of data
version	character, data source version
server	character, data source links
fp	character vector, add fluoresecent proteins info

Value

a list, contains txdb, tx2gene, annotation

Examples

GRCh38 <- gtf_to_annotation("Homo_sapiens.GRCh38.95.gtf", species="hs", geonme="GRCh38")
GRCh38_txdb <- GRCh38$txdb
AnnotationDbi::saveDb(GRCh38_txdb, "txdb.ensembl.95.GRCh38.sqlite")
GRCh38_tx2gene <- GRCh38$tx2gene
GRCh38_annotation <- GRCh38$annotation

soulong/annoHub documentation built on May 12, 2020, 7:22 a.m.