ImportCpGIslandExt: Import CpG-islands from UCSC genomes

In benja0x40/Tightrope: ChIP-seq normalization according to background reads density

Description

Import CpG-islands from UCSC genomes

Usage

ImportCpGIslandExt(genome = NULL, fpath = NULL,
  goldenPath = "http://hgdownload.soe.ucsc.edu/goldenPath",
  cpgIslandExt = "database/cpgIslandExt.txt.gz", keep.file = FALSE,
  quiet = FALSE)

Arguments

genome	name of an UCSC genome build. When genome is unspecified, the fpath argument must be specified.
fpath	path to a cpgIslandExt.txt.gz file. When fpath is unspecified, the genome argument must be specified.
goldenPath	base URL of UCSC genome repositories (default = "http://hgdownload.soe.ucsc.edu/goldenPath").
cpgIslandExt	path to cpgIslandExt.txt.gz files in the UCSC genome repositories (default = "database/cpgIslandExt.txt.gz").
keep.file	logical value controlling whether the downloaded file should be kept or deleted (default = FALSE, delete).
...	optional parameters forwarded to the ImportGenomicRanges function.

Value

ImportCpGIslandExt returns a GRanges object.

See Also

ImportGenomicRanges, CleanupGRanges, ReadCountMatrix

benja0x40/Tightrope documentation built on May 24, 2019, 1:35 a.m.