README.md

In metamaden/rmpipeline: Process DNAm array IDATs into database files

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).

metamaden/rmpipeline documentation built on Jan. 12, 2023, 3:20 p.m.