downloadDB: Download database files from public genome database server

In bioinfo16/IRFinder: Vector integrated region analysis package (IRFinder)

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('Repeat', 'CpG', 'Gap'), organism = 'hg19', 
                  dbPath = paste0(.libPaths()[1], '/IRFinder/extdata'))

Arguments

dbtype	an array or vector. Avaliable values are 'Repeat', 'CpG' and 'Gap'. Repeat : Repeat database file made by Repeatmasker. CpG : It means CpG islands. 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/IRFinder documentation built on Aug. 19, 2019, 10:37 a.m.