build_Ensembl_reference: Build Ensembl database reference

In HatsuneCode/TrustVDJ: Tools for Immune Repertoire Analysis

Build Ensembl database reference

Description

Download latest reference files (.fa and .gtf) from Ensembl database and split the files by species.

Usage

build_Ensembl_reference(
  outdir = NULL,
  species = NULL,
  method = NULL,
  ftp_method = NULL,
  verbose = TRUE
)

Arguments

outdir	character. Default getwd()
species	character. Default 'ALL'
method	character. Method to be used for downloading html files, equal to download.file. Default 'libcurl'
ftp_method	character. Method to be used for downloading ftp files (.fa and .gtf), equal to download.file. Default 'curl'
verbose	logical. Default TRUE

Value

if success, return TRUE

Examples

build_Ensembl_reference('Ensembl_ref', 'acanthochromis_polyacanthus')

HatsuneCode/TrustVDJ documentation built on Aug. 13, 2022, 9:36 p.m.