### R code from vignette source 'vignettes/ADaCGH2/inst/doc/ADaCGH2-long-examples.Rnw' ### Encoding: UTF-8 ################################################### ### code chunk number 1: ADaCGH2-long-examples.Rnw:107-108 ################################################### try(setwd("~/tmp")) ################################################### ### code chunk number 2: ADaCGH2-long-examples.Rnw:111-148 ################################################### library(ADaCGH2) ## loading in-RAM objects data(inputEx) summary(inputEx) head(inputEx) cgh.dat <- inputEx[, -c(1, 2, 3)] chrom.dat <- as.integer(inputEx[, 2]) pos.dat <- inputEx[, 3] ## choosing working dir for cluster originalDir <- getwd() if(!file.exists("ADaCGH2_vignette_tmp_dir")) dir.create("ADaCGH2_vignette_tmp_dir") setwd("ADaCGH2_vignette_tmp_dir") ## creating ff objects fnameRdata <- list.files(path = system.file("data", package = "ADaCGH2"), full.names = TRUE, pattern = "inputEx.RData") inputToADaCGH(ff.or.RAM = "ff", RDatafilename = fnameRdata) ## initializing cluster number.of.nodes <- detectCores() cl2 <- parallel::makeCluster(number.of.nodes,"PSOCK") parallel::clusterSetRNGStream(cl2) parallel::setDefaultCluster(cl2) parallel::clusterEvalQ(NULL, library("ADaCGH2")) ## verify we are using the right version of ADaCGH2 parallel::clusterEvalQ(NULL, library(help = ADaCGH2)$info[[1]][[2]]) wdir <- getwd() parallel::clusterExport(NULL, "wdir") parallel::clusterEvalQ(NULL, setwd(wdir)) ################################################### ### code chunk number 3: ADaCGH2-long-examples.Rnw:176-229 ################################################### cbs.mergel.RAM.fork <- pSegmentDNAcopy(cgh.dat, chrom.dat, merging = "mergeLevels") cbs.mad.RAM.fork <- pSegmentDNAcopy(cgh.dat, chrom.dat,merging = "MAD") cbs.none.RAM.fork <- pSegmentDNAcopy(cgh.dat, chrom.dat, merging = "none") hmm.mergel.RAM.fork <- pSegmentHMM(cgh.dat, chrom.dat, merging = "mergeLevels") hmm.mad.RAM.fork <- pSegmentHMM(cgh.dat, chrom.dat, merging = "MAD") hs.mergel.RAM.fork <- pSegmentHaarSeg(cgh.dat, chrom.dat, merging = "mergeLevels") hs.mad.RAM.fork <- pSegmentHaarSeg(cgh.dat, chrom.dat, merging = "MAD") hs.none.RAM.fork <- pSegmentHaarSeg(cgh.dat, chrom.dat, merging = "none") glad.RAM.fork <- pSegmentGLAD(cgh.dat, chrom.dat) biohmm.mergel.RAM.fork <- pSegmentBioHMM(cgh.dat, chrom.dat, pos.dat, merging = "mergeLevels") biohmm.mad.RAM.fork <- pSegmentBioHMM(cgh.dat, chrom.dat, pos.dat, merging = "MAD") biohmm.mad.bic.RAM.fork <- pSegmentBioHMM(cgh.dat, chrom.dat, pos.dat, merging = "MAD", aic.or.bic = "BIC") cghseg.mergel.RAM.fork <- pSegmentCGHseg(cgh.dat, chrom.dat, merging = "mergeLevels") cghseg.mad.RAM.fork <- pSegmentCGHseg(cgh.dat, chrom.dat, merging = "MAD") cghseg.none.RAM.fork <- pSegmentCGHseg(cgh.dat, chrom.dat, merging = "none") waves.mergel.RAM.fork <- pSegmentWavelets(cgh.dat, chrom.dat, merging = "mergeLevels") waves.mad.RAM.fork <- pSegmentWavelets(cgh.dat, chrom.dat, merging = "MAD") waves.none.RAM.fork <- pSegmentWavelets(cgh.dat, chrom.dat, merging = "none") ################################################### ### code chunk number 4: ADaCGH2-long-examples.Rnw:253-331 ################################################### cbs.mergel.ff.cluster <- pSegmentDNAcopy("cghData.RData", "chromData.RData", merging = "mergeLevels", typeParall = "cluster") cbs.mad.ff.cluster <- pSegmentDNAcopy("cghData.RData", "chromData.RData", merging = "MAD", typeParall = "cluster") cbs.none.ff.cluster <- pSegmentDNAcopy("cghData.RData", "chromData.RData", merging = "none", typeParall = "cluster") hmm.mergel.ff.cluster <- pSegmentHMM("cghData.RData", "chromData.RData", merging = "mergeLevels", typeParall = "cluster") hmm.mad.ff.cluster <- pSegmentHMM("cghData.RData", "chromData.RData", merging = "MAD", typeParall = "cluster") hs.mergel.ff.cluster <- pSegmentHaarSeg("cghData.RData", "chromData.RData", merging = "mergeLevels", typeParall = "cluster") hs.mad.ff.cluster <- pSegmentHaarSeg("cghData.RData", "chromData.RData", merging = "MAD", typeParall = "cluster") hs.none.ff.cluster <- pSegmentHaarSeg("cghData.RData", "chromData.RData", merging = "none", typeParall = "cluster") glad.ff.cluster <- pSegmentGLAD("cghData.RData", "chromData.RData", typeParall = "cluster") biohmm.mergel.ff.cluster <- pSegmentBioHMM("cghData.RData", "chromData.RData", "posData.RData", merging = "mergeLevels", typeParall = "cluster") biohmm.mad.ff.cluster <- pSegmentBioHMM("cghData.RData", "chromData.RData", "posData.RData", merging = "MAD", typeParall = "cluster") biohmm.mad.bic.ff.cluster <- pSegmentBioHMM("cghData.RData", "chromData.RData", "posData.RData", merging = "MAD", aic.or.bic = "BIC", typeParall = "cluster") cghseg.mergel.ff.cluster <- pSegmentCGHseg("cghData.RData", "chromData.RData", merging = "mergeLevels", typeParall = "cluster") cghseg.mad.ff.cluster <- pSegmentCGHseg("cghData.RData", "chromData.RData", merging = "MAD", typeParall = "cluster") cghseg.none.ff.cluster <- pSegmentCGHseg("cghData.RData", "chromData.RData", merging = "none", typeParall = "cluster") waves.mergel.ff.cluster <- pSegmentWavelets("cghData.RData", "chromData.RData", merging = "mergeLevels", typeParall = "cluster") waves.mad.ff.cluster <- pSegmentWavelets("cghData.RData", "chromData.RData", merging = "MAD", typeParall = "cluster") waves.none.ff.cluster <- pSegmentWavelets("cghData.RData", "chromData.RData", merging = "none", typeParall = "cluster") ################################################### ### code chunk number 5: ADaCGH2-long-examples.Rnw:352-424 ################################################### cbs.mergel.ff.fork <- pSegmentDNAcopy("cghData.RData", "chromData.RData", merging = "mergeLevels", typeParall = "fork") cbs.mad.ff.fork <- pSegmentDNAcopy("cghData.RData", "chromData.RData", merging = "MAD", typeParall = "fork") cbs.none.ff.fork <- pSegmentDNAcopy("cghData.RData", "chromData.RData", merging = "none", typeParall = "fork") hmm.mergel.ff.fork <- pSegmentHMM("cghData.RData", "chromData.RData", merging = "mergeLevels", typeParall = "fork") hmm.mad.ff.fork <- pSegmentHMM("cghData.RData", "chromData.RData", merging = "MAD", typeParall = "fork") hs.mergel.ff.fork <- pSegmentHaarSeg("cghData.RData", "chromData.RData", merging = "mergeLevels", typeParall = "fork") hs.mad.ff.fork <- pSegmentHaarSeg("cghData.RData", "chromData.RData", merging = "MAD", typeParall = "fork") hs.none.ff.fork <- pSegmentHaarSeg("cghData.RData", "chromData.RData", merging = "none", typeParall = "fork") glad.ff.fork <- pSegmentGLAD("cghData.RData", "chromData.RData", typeParall = "fork") biohmm.mergel.ff.fork <- pSegmentBioHMM("cghData.RData", "chromData.RData", "posData.RData", merging = "mergeLevels", typeParall = "fork") biohmm.mad.ff.fork <- pSegmentBioHMM("cghData.RData", "chromData.RData", "posData.RData", merging = "MAD", typeParall = "fork") biohmm.mad.bic.ff.fork <- pSegmentBioHMM("cghData.RData", "chromData.RData", "posData.RData", merging = "MAD", aic.or.bic = "BIC", typeParall = "fork") cghseg.mergel.ff.fork <- pSegmentCGHseg("cghData.RData", "chromData.RData", merging = "mergeLevels", typeParall = "fork") cghseg.mad.ff.fork <- pSegmentCGHseg("cghData.RData", "chromData.RData", merging = "MAD", typeParall = "fork") cghseg.none.ff.fork <- pSegmentCGHseg("cghData.RData", "chromData.RData", merging = "none", typeParall = "fork") waves.merge.ff.fork <- pSegmentWavelets("cghData.RData", "chromData.RData", merging = "mergeLevels", typeParall = "fork") waves.mad.ff.fork <- pSegmentWavelets("cghData.RData", "chromData.RData", merging = "MAD", typeParall = "fork") waves.none.ff.fork <- pSegmentWavelets("cghData.RData", "chromData.RData", merging = "none", typeParall = "fork") ################################################### ### code chunk number 6: ADaCGH2-long-examples.Rnw:442-443 ################################################### ff.cluster.obj <- ls(pattern = "*.ff.cluster") ################################################### ### code chunk number 7: ADaCGH2-long-examples.Rnw:447-451 ################################################### tmpout <- capture.output( lapply(ff.cluster.obj, function(x) lapply(get(x), open)) ) ################################################### ### code chunk number 8: ADaCGH2-long-examples.Rnw:457-463 ################################################### ff.fork.obj <- ls(pattern = "*.ff.fork") tmpout <- capture.output( lapply(ff.fork.obj, function(x) lapply(get(x), open)) ) ################################################### ### code chunk number 9: ADaCGH2-long-examples.Rnw:471-472 ################################################### RAM.fork.obj <- ls(pattern = "*.RAM.fork") ################################################### ### code chunk number 10: ADaCGH2-long-examples.Rnw:533-551 ################################################### identical3 <- function(x, y, z) { comp1 <- all.equal(get(x)$outSmoothed[ , ], get(y)$outSmoothed[ , ]) comp2 <- all.equal(get(y)$outSmoothed[ , ], get(z)$outSmoothed[ , ]) comp3 <- identical(get(x)$outState[ , ], get(y)$outState[ , ]) comp4 <- identical(get(y)$outState[ , ], get(z)$outState[ , ]) if (!all(isTRUE(comp1), isTRUE(comp2), comp3, comp4)) { cat(paste("Comparing ", x, y, z, "\n", "not equal: some info from comparisons.\n", "\n comp1 = ", paste(comp1, sep = " ", collapse = "\n "), "\n comp2 = ", paste(comp2, sep = " ", collapse = "\n "), "\n comp3 = ", paste(comp3, sep = " ", collapse = "\n "), "\n comp4 = ", paste(comp4, sep = " ", collapse = "\n "), "\n\n")) return(FALSE) } else { TRUE } } ################################################### ### code chunk number 11: ADaCGH2-long-examples.Rnw:576-579 ################################################### mapply(identical3, RAM.fork.obj, ff.fork.obj, ff.cluster.obj) ################################################### ### code chunk number 12: ADaCGH2-long-examples.Rnw:653-654 ################################################### parallel::stopCluster(cl2) ################################################### ### code chunk number 13: ADaCGH2-long-examples.Rnw:657-687 (eval = FALSE) ################################################### ## ## This is the code to remove all the files we created ## ## and the temporary directory. ## ## We are not executing it! ## ## load("chromData.RData") ## load("posData.RData") ## load("cghData.RData") ## ## delete(cghData); rm(cghData) ## delete(posData); rm(posData) ## delete(chromData); rm(chromData) ## ## tmpout <- ## capture.output( ## lapply(ff.fork.obj, function(x) { ## lapply(get(x), delete)})) ## ## rm(list = ff.fork.obj) ## ## tmpout <- ## capture.output( ## lapply(ff.cluster.obj, function(x) { ## lapply(get(x), delete)})) ## rm(list = ff.cluster.obj) ## ## setwd(originalDir) ## print(getwd()) ## Sys.sleep(3) ## unlink("ADaCGH2_vignette_tmp_dir", recursive = TRUE) ## Sys.sleep(3)