downloadDB: Download database files from public genome database server

In bioinfo16/VVIPS: Viral Vector Integration Position Seeker

Description

This function should be excuted before running annotation functions. By this function, user can download genome database file from UCSC and ENSEMBL database. User can download 5 types of human-related database and 4 types of chicken-related database. Function connects ucsc server to download repeats, CpG island and annotated gap database file. Plus, ENSEMBL data fils are also downloaded to annotate about transcription start site and genomic site.

Usage

downloadDB(dbtype = c('Gene', 'Repeat', 'CpG', 'Gap'), organism = 'hg19', 
                  dbPath = paste0(.libPaths()[1], '/VVIPS/extdata'))

Arguments

dbtype	an array or vector. Avaliable values are 'Gene', 'Repeat', 'CpG' and 'Gap'. "Gene"Gene database includes transcription start sites. "Repeat"Repeat database file made by Repeatmasker. "CpG"CpG database includes the number of CpG site and GC ratio "Gap"This data is about annotated gaps. By this data, Annotation regions about centromere, telomere and heterochromatin is possible. That is provided by UCSC genome browser.
organism	a single character. This function serves 3 versions of organisms such as hg19, hg38 (Human) and galGal6 (Chicken).
dbPath	a string vector. Path for saving database files.

bioinfo16/VVIPS documentation built on Nov. 4, 2019, 7:20 a.m.