Mercurial > repos > testtool > find_dmp
annotate findDMP/findDMP.R @ 0:8cf72c018b42 draft default tip
Uploaded
| author | testtool |
|---|---|
| date | Sun, 11 Jun 2017 17:29:26 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| 0 | 1 require("minfi", quietly = TRUE) |
| 2 require("data.table", quietly = TRUE) | |
| 3 | |
| 4 options(warn = -1) | |
| 5 options("download.file.method"="wget") | |
| 6 | |
| 7 args <- commandArgs(trailingOnly = TRUE) | |
| 8 | |
| 9 input1 = args[1] | |
| 10 input2 = args[2] | |
| 11 output = args[3] | |
| 12 | |
| 13 GRset <- get(load(input1)) | |
| 14 | |
| 15 pheno <- read.csv(input2) | |
| 16 | |
| 17 beta <- getBeta(GRset) | |
| 18 | |
| 19 pData <- pData(GRset) | |
| 20 | |
| 21 dmp <- dmpFinder(beta, pheno$Phenotype, type = "continuous") | |
| 22 | |
| 23 write.table(dmp, output) |