ChAMP (version 1.10.0)

champ.MVP: Identify Most Variable Positions in Illumina HumanMethylation450 data.

Description

This function

Usage

champ.MVP(beta.norm = myNorm$beta, pd = myLoad$pd, adjPVal = 0.05, adjust.method = "BH", 
compare.group = c("C", "T"), resultsDir = paste(getwd(), "resultsChamp", sep = "/"), 
bedFile = TRUE,arraytype="450K")

Arguments

beta.norm

A matrix of values representing the methylation scores for each sample (M or B). The default assumes you ran champ.norm and saved the output to "norm".

pd

This data.frame includes the information from the sample sheet. The default assumes you ran champ.load and saved the output to "myLoad".

adjPVal

The minimum threshold of significance for probes to be considered an MVP, default = 0.05

adjust.method

The p-value adjustment method to be used for the limma analyis, default= BH (Benjamini-Hochberg)

compare.group

Not yet implemented

resultsDir

Directory where results will be saved. Default is a folder in the current working directory called "resultsChamp".

bedFile

If bedFile=TRUE, the MVPs will be saved in bedfile format for downstream analysis.

arraytype

Choose microarray type is 450K or EPIC.

Value

results.file

A matrix of all probes with an adjusted p-value for significance of differential methylation containing columns for probeID, logFC, AveExpr, t, P.Value, adjusted p-value, B, chromosome, map info, chromosome arm, closest gene.1, gene.2, gene.3, gene.4, closest feature.1, feature.2, feature.3, feature.4, UCSC_CpG_ISLANDS_NAME, Relation to UCSC CpG Island, Phantom, DMR, Enhancer, HMM_Island, regulatory feature name, regulatory feature group, feature relation, average of first sample group, average of second sample group, delta beta