rm(list = ls())
library(dplyr)
library(ccube)
library(doParallel)
library(ggplot2)
library(tidyr)
library(gridExtra)
options(stringsAsFactors = F)
registerDoParallel(cores=3)
set.seed(1234)
numOfClusterPool = 1:7
numOfRepeat = 10
icgc <- "~/debug_pcawg_samples_sv/svclone_paper_20181127/"
dataFolders <- dir(icgc, full.names = T)
sampleNames <- dir(icgc)
bugSamples <- c()
bugdataFolders <- c()
for (ii in seq_along(sampleNames)) {
sampleName <- sampleNames[ii]
dataFolder <- dataFolders[ii]
if (! "ccube_out/ccube_sv_results.RData" %in% dir(dataFolder, recursive = T) ) {
bugSamples <- c(bugSamples, sampleName)
bugdataFolders <- c(bugdataFolders, dataFolder)
}
}
allDebugFolder <- "~/debug_pcawg_samples_sv/debuged_samples"
problemSamples <- c("36e1d9cc-32ec-4a0a-8fb1-c46f058a6fb8", "60413de1-6cd2-4f74-8180-3bdd394d6d16",
"7dc5f8ba-0080-43d3-8426-bd527a970761", "7eac4710-c622-11e3-bf01-24c6515278c0",
"ea43434b-197e-48ac-ae2e-46bc7f3776de", "fc249113-83d4-4abe-8c80-a4f7305dcd91")
ii = which(sampleNames == problemSamples[6])
cat(ii, "\n")
sampleName <- sampleNames[ii]
dataFolder <- dataFolders[ii]
resultsFolder <- paste0(allDebugFolder,"/", sampleName)
if (! dir.exists(resultsFolder) ) {
dir.create(resultsFolder, recursive = T)
}
inputFn <- paste0(dataFolder, "/", sampleName, "_ccube_sv_input.txt")
mydata <- try( read.delim(inputFn), T)
ccubeRes <-
RunCcubePipeline(ssm = mydata, modelSV = T,
numOfClusterPool = numOfClusterPool,
numOfRepeat = numOfRepeat, multiCore =T,
runAnalysisSnap = T, runQC = T, maxiter = 10)
fn = paste0(resultsFolder, "/ccube_sv_results.RDdata")
save(ccubeRes, file = fn)
fn = paste0(resultsFolder, "/ccube_sv_results.pdf")
MakeCcubeStdPlot_sv(res = ccubeRes$res, ssm = ccubeRes$ssm, printPlot = T, fn = fn)
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