recountmethylation.pipeline

Functions and utilities to compile and harmonize public GEO DNA methylation array datasets. This includes generation of the assay compilation objects as HDF5 and HDF5-SummarizedExperiment objects, as well as metadata mappings and predictions for sample metadata from study SOFT files. To see implementation, see the recountmethylation_instance resource.

Install

Devtools install

Install this package from an R session using the devtools R package with:

devtools::install_github("metamaden/rmpipeline")

Manual install

Obtain this package from github with:

git clone https://www.github.com/metamaden/recountmethylation.pipeline

Install the cloned repo using:

R CMD INSTALL recountmethylation.pipeline

Load

After installation, load this package into an active R session library(recountmethylation.pipeline).