Hi guys,
I just got this weird error with CNTools package. Basically I tried to map TCGA SNP6 level3 segmentation data to gene level. I have TCGA SNP6 level3 segmentation data fpor more than 16000 samples. All processed well except for a block of 300 samples, which gave me the following error message:
> library(CNTools)> load("tcgaSNP6_df.RData")> sampleData <- data.frame(ID=df$sample,chrom=df$chromosome,loc.start=df$start,loc.end=df$stop,num.mark=df$count,seg.mean=df$mean)> sampleData$ID <- as.character(sampleData$ID)> sampleData$chrom <- as.character(sampleData$chrom)> geneInfo <- read.delim("geneMap.txt")> sessionInfo()R version 3.0.2 (2013-09-25)Platform: x86_64-unknown-linux-gnu (64-bit)
locale: [1] LC_CTYPE=en_US       LC_NUMERIC=C         LC_TIME=en_US        [4] LC_COLLATE=en_US     LC_MONETARY=en_US    LC_MESSAGES=en_US    [7] LC_PAPER=en_US       LC_NAME=C            LC_ADDRESS=C        [10] LC_TELEPHONE=C       LC_MEASUREMENT=en_US LC_IDENTIFICATION=C 
attached base packages:[1] tools     stats     graphics  grDevices utils     datasets  methods  [8] base     
other attached packages:[1] CNTools_1.18.0    genefilter_1.44.0
loaded via a namespace (and not attached): [1] annotate_1.40.0      AnnotationDbi_1.24.0 Biobase_2.22.0       [4] BiocGenerics_0.8.0   DBI_0.2-7            IRanges_1.20.0       [7] parallel_3.0.2       RSQLite_0.11.4       splines_3.0.2       [10] stats4_3.0.2         survival_2.37-4      XML_3.98-1.1        [13] xtable_1.7-1        > cnseg <- CNSeg(sampleData[which(is.element(sampleData[, "ID"], unique(sampleData[, "ID"])[7201:7500])), ])> rdByGene <- getRS(cnseg, by = "gene", imput = FALSE, XY = FALSE, geneMap = geneInfo, what = "median")
 *** caught segfault ***address (nil), cause 'unknown'
Traceback: 1: .C("getratios", as.character(map[, mapChrom]), as.double(map[,     mapStart]), as.double(map[, mapEnd]), as.integer(nrow(map)),     as.character(segData[, segChrom]), as.double(segData[, segStart]),     as.double(segData[, segEnd]), as.integer(nrow(segData)),     as.double(segData[, segMean]), as.character(what), as.double(segged),     PACKAGE = "CNTools") 2: FUN(X[[1L]], ...) 3: lapply(splited, getGeneSegMean) 4: do.call("cbind", args = lapply(splited, getGeneSegMean)) 5: cbind(map, do.call("cbind", args = lapply(splited, getGeneSegMean))) 6: getReducedSeg(segList(segData), geneMap, what = what, segID = id(segData),     segChrom = chromosome(segData), segStart = start(segData),     segEnd = end(segData), segMean = segMean(segData), mapChrom = mapChrom,     mapStart = mapStart, mapEnd = mapEnd) 7: seg2RS(object, by, imput, XY, geneMap, what = what, mapChrom = mapChrom,     mapStart = mapStart, mapEnd = mapEnd) 8: getRS(cnseg, by = "gene", imput = FALSE, XY = FALSE, geneMap = geneInfo,     what = "median") 9: getRS(cnseg, by = "gene", imput = FALSE, XY = FALSE, geneMap = geneInfo,     what = "median")
Possible actions:1: abort (with core dump, if enabled)2: normal R exit3: exit R without saving workspace4: exit R saving workspaceSelection: > 
Any suggestion?
Thanks a lot for the help!
Ying 		 	   		  
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