getRandomPairs {ELMER} | R Documentation

## Get random pairs

### 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)

[Package ELMER version 2.16.0 Index]