AnnotateResults: Annotate 'coMethDMR' Pipeline Results

In lissettegomez/coMethDMR: Accurate identification of co-methylated and differentially methylated regions in epigenome-wide association studies

Description

Given a data frame with regions in the genome, add gene symbols, UCSC reference gene accession, UCSC reference gene group and relation to CpG island.

Usage

AnnotateResults(lmmRes_df, arrayType = c("450k", "EPIC"), nCores_int = 1L, ...)

Arguments

lmmRes_df	A data frame returned by lmmTestAllRegions. This data frame must contain the following columns: chrom : the chromosome the region is on, e.g. “chr22” start : the region start point end : the region end point Optionally, the data frame can also has regionType, which is a character string marking the type of genomic region tested. See details below.
arrayType	Type of array: 450k or EPIC
nCores_int	Number of computing cores to be used when executing code in parallel. Defaults to 1 (serial computing).
...	Dots for additional arguments passed to the cluster constructor. See CreateParallelWorkers for more information.

Details

The region types include "NSHORE", "NSHELF", "SSHORE", "SSHELF", "TSS1500", "TSS200", "UTR5", "EXON1", "GENEBODY", "UTR3", and "ISLAND".

Value

A data frame with

• the location of the genomic region's chromosome (chrom), start (start), and end (end);

• UCSC annotation information (UCSC_RefGene_Group, UCSC_RefGene_Accession, and UCSC_RefGene_Name); and

• a list of all of the probes in that region (probes).

Examples

   lmmResults_df <- data.frame(
     chrom = c("chr22", "chr22", "chr22", "chr22", "chr22"),
     start = c("39377790", "50987294", "19746156", "42470063", "43817258"),
     end   = c("39377930", "50987527", "19746368", "42470223", "43817384"),
     regionType = c("TSS1500", "EXON1", "ISLAND", "TSS200", "ISLAND"),
     stringsAsFactors = FALSE
   )

   AnnotateResults(
     lmmRes_df = lmmResults_df,
     arrayType = "450k"
   )

lissettegomez/coMethDMR documentation built on April 25, 2021, 1:10 p.m.