get.permu {ELMER} | R Documentation |
get.permu is a function to use the same statistic model to calculate random enhancer-gene pairs. Based on the permutation value, empirical P value can be calculated for the real enhancer-gene pair (see reference).
get.permu(data, geneID, methy = NULL, unmethy = NULL, percentage = 0.2, rm.probes = NULL, permu.size = 10000, permu.dir = NULL, cores = 1)
data |
A multiAssayExperiment with DNA methylation and Gene Expression data. See |
geneID |
A vector lists the genes' ID. |
methy |
Index of M (methylated) group. |
unmethy |
Index of U (unmethylated) group. |
percentage |
A number ranges from 0 to 1 specifying the percentage of samples of group 1 and group 2 groups used to link probes to genes. Default is 0.2. |
rm.probes |
A vector lists the probes name. |
permu.size |
A number specify the times of permuation. Default is 10000. |
permu.dir |
A path where the output of permuation will be. |
cores |
A interger which defines number of core to be used in parallel process. Default is 1: don't use parallel process. |
Permutations
Permutation is the most time consuming step. It is recommended to use multiple cores for this step. Default permutation time is 1000 which may need 12 hrs by 4 cores. However 10,000 permutations is recommended to get high confidence results. But it may cost 2 days.
Lijing Yao (creator: lijingya@usc.edu) Tiago C Silva (maintainer: tiagochst@usp.br)
Yao, Lijing, et al. "Inferring regulatory element landscapes and transcription factor networks from cancer methylomes." Genome biology 16.1 (2015): 1.
data <- ELMER:::getdata("elmer.data.example") permu <-get.permu(data = data, geneID=rownames(getExp(data)), rm.probes=c("cg00329272","cg10097755"), permu.size=5)