View source: R/Merge_methylation.R
methyDiff_ucsc | R Documentation |
Title
methyDiff_ucsc( methy, sampleGroup = NULL, missing_value = "knn", model = c("cpg", "gene"), combineMethod = RobustRankAggreg::rhoScores, region = "Body" )
methy |
data.frame of the methylation data, which can be downloaded from UCSC Xena. |
sampleGroup |
a vector of "0" and "1" for group of samples. If null, the samples were divided into two groups: disease and normal. |
missing_value |
Method to impute missing expression data, one of "zero" and "knn". |
model |
if "cpg", step1: calculate difference cpgs; step2: calculate difference genes. if "gene", step1: calculate the methylation level of genes; step2: calculate difference genes. |
combineMethod |
method to combine the cpg pvalues. |
region |
region of genes, one of "Body", "TSS1500", "TSS200", "3'UTR", "1stExon", "5'UTR", and "IGR". |
## Not run: methy_file <- "TCGA.THCA.sampleMap_HumanMethylation450.gz" methy <- data.table::fread(methy_file, sep = "\t", header = T) library(ChAMP) myImport <- champ.import(directory=system.file("extdata",package="ChAMPdata")) myfilter <- champ.filter(beta=myImport$beta,pd=myImport$pd, detP=myImport$detP,beadcount=myImport$beadcount) cpg_gene <- hm450.manifest.hg19[, c("probeID", "gene_HGNC")] result <- methyDiff_ucsc(methy, cpg_gene) ## End(Not run)
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