getRandomPairs {ELMER} | R Documentation |
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.
getRandomPairs(pairs, genome = "hg38", met.platform = "450K", cores = 1)
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. |
A data frame with the random linkages
## 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)