GeoTcgaData (version 1.1.1.992)

methyDiff: Get methylation difference gene

Description

Get methylation difference gene

Usage

methyDiff(
  cpgData,
  sampleGroup,
  combineMethod = RobustRankAggreg::rhoScores,
  missing_value = "knn",
  region = "Body",
  model = "cpg",
  adjust.method = "BH"
)

Arguments

cpgData

data.frame of cpg beta value

sampleGroup

vector of sample group

combineMethod

method to combine the cpg pvalues

missing_value

Method to impute missing expression data, one of "zero" and "knn".

region

region of genes, one of "Body", "TSS1500", "TSS200", "3'UTR", "1stExon", "5'UTR", and "IGR".

model

if "cpg", step1: calculate difference cpgs; step2: calculate difference genes. if "gene", step1: calculate the methylation level of genes; step2: calculate difference genes.

adjust.method

character string specifying the method used to adjust p-values for multiple testing. See p.adjust for possible values.