DecompPipeline

Large automated pipeline for running MeDeCom

Installing DecompPipeline

DecompPipeline can be directly installed from GitHub within an R session:

install.packages("devtools")
devtools::install_github("lutsik/DecompPipeline")

Using Decomp

DecompPipeline includes three major steps, all of them are extensively documented. A more detailed introduction into DecompPipeline can be found in the package vignette.

CpG filtering

There are dedicated preprocessing steps for both array-based data sets (prepare_data) and sequencing-based data sets (prepare_data_BS).

Selecting CpG subsets

To select a subset of CpGs for downstream MeDeCom analysis, the function prepare_CG_subsets can be used.

Starting MeDeCom

After these preprocessing steps, a MeDeCom run can be started using DecompPipeline by envoking start_decomp_pipeline.

Combining the above steps

We also provide a wrapper functions that executes all the above steps in a single command (start_decomp_pipeline).