getRandomPairs: Get random pairs

In ELMER: Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

Description

This function will receive a pair gene probes and will return a random object with the following pattern, if a probe is linked to R1 and L3 genes the random pairs will be a random probes (a distal probe not in the input pairs) also linked to its R1 and L3 gene.

Usage

getRandomPairs(pairs, genome = "hg38", met.platform = "450K", cores = 1)

Arguments

pairs	A data frame with probe, gene and side information. See example below.
genome	Which genome build will be used: hg38 (default) or hg19.
met.platform	DNA methyaltion platform to retrieve data from: EPIC or 450K (default)
cores	A interger which defines the number of cores to be used in parallel process. Default is 1: no parallel process.

Value

A data frame with the random linkages

Examples

## Not run: 
 data <- ELMER:::getdata("elmer.data.example")
 nearGenes <- GetNearGenes(TRange=getMet(data)[c("cg00329272","cg10097755"),],
                            geneAnnot=getExp(data))
                            
 pair <- get.pair(data = data,
                  group.col = "definition", 
                  group1 = "Primary solid Tumor", 
                  group2 = "Solid Tissue Normal",
                  mode = "supervised",
                  diff.dir = "hypo",
                  nearGenes = nearGenes,
                  permu.size = 5,
                  raw.pvalue =  0.001,
                  Pe = 0.2,
                  dir.out="./",
                  permu.dir = "permu_test",
                  label = "hypo")

## End(Not run)
 pair <- data.frame(Probe = rep("cg00329272",3), 
                    GeneID = c("ENSG00000116213","ENSG00000130762","ENSG00000149527"),
                    Sides = c("R5","R2","L4"))                    
 getRandomPairs(pair)

ELMER documentation built on Nov. 8, 2020, 4:59 p.m.