rnb.read.geo: Import methylation data from GEO

Description Usage Arguments Value Author(s)

View source: R/readGEO.R

Description

Imports Infinium 450K or MethylationEPIC data series from the Gene Expression Omnibus. This function uses the series matrix file.

Usage

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rnb.read.geo(accession = NULL, verbose = logger.isinitialized(),
  destdir = tempdir())

Arguments

accession

Character string, starting with "GSE", representing the GEO series for download and parsing. Alternatively, this parameter can specify the file name of a previously downloaded GEO series matrix file or its gzipped representation (in which case the filename must end in ".gz"). Other file formats, such as SOFT files, are not supported.

verbose

Flag indicating if messages should be created informing about the progress. If the logger is initialized prior to calling this function, the informative messages are sent to the logger. Warnings and errors are not affected by this parameters, the function always outputs them.

destdir

The destination directory for any downloads. Defaults to the (architecture-dependent) temporary directory. Keep in mind that GEO series can be demanding in terms of storage space.

Value

RnBeadSet object with phenotypic and beta value information.

Author(s)

Yassen Assenov


RnBeads documentation built on Nov. 1, 2018, 2:16 a.m.