methyDiff: Get methylation difference gene

In GeoTcgaData: Processing various types of data on GEO and TCGA

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.

GeoTcgaData documentation built on Sept. 23, 2022, 9:05 a.m.