Segfault in MEDIPS MEDIPS.methylProfiling() with ROI file
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@stephen-turner-4916
Last seen 5.7 years ago
United States
Lukas, and others: I'm trying to use the MEDIPS package to look for differentially methylated regions, supplying a regions of interest file (essentially a bed file). I was able to successfully run MEDIPS.methylProfiling supplying the frame_size=500 argument to look for DMRs in 500-bp windows. Now I'd like to supply my own regions of interest to look for DMR around genes that are differentially expressed from microarray. I get the following segfault: ############### > dmrGenes <- MEDIPS.methylProfiling(data1=CONTROL.SET, data2=BPA.SET, ROI_file="ROI_file.txt", select=2) Preprocessing... Reading ROIs... Extract data according to given ROI... Differential methylation will be calculated on the ROI data set Analysed 379 / 2893 *** caught segfault *** address 0x2b61ee9d5e98, cause 'memory not mapped' Traceback: 1: .Call("roiprofile", input, as.numeric(select), as.matrix(ROI2), as.integer(chr_binposition), data1, data2, environment(wilcox.test), wilcox.test, environment(var), var, environment(math), math, t.test, environment(t.test), as.numeric(factor(chr_names(data1)))) 2: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning")) 3: suppressWarnings(.Call("roiprofile", input, as.numeric(select), as.matrix(ROI2), as.integer(chr_binposition), data1, data2, environment(wilcox.test), wilcox.test, environment(var), var, environment(math), math, t.test, environment(t.test), as.numeric(factor(chr_names(data1))))) 4: MEDIPS.methylProfiling(data1 = CONTROL.SET, data2 = BPA.SET, ROI_file = "ROI_file.txt", select = 2) aborting ... ############### I ran this on a machine with 128GB RAM, so I know that wasn't the problem. It looks like the segfault was happening with line 379 in the sample above. I went into the regions of interest (ROI) file containing gene coordinates. Nothing looked weird about this line, but I deleted it anyway. When re-running, I still get segfaults, just at different positions. Thanks for any insight you might have. Stephen > sessionInfo() R version 2.15.2 (2012-10-26) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BSgenome.Mmusculus.UCSC.mm9_1.3.19 MEDIPS_1.8.0 [3] BSgenome_1.26.1 Biostrings_2.26.3 [5] GenomicRanges_1.10.6 IRanges_1.16.4 [7] BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] gtools_2.7.0 parallel_2.15.2 stats4_2.15.2
Microarray BSgenome BSgenome MEDIPS Microarray BSgenome BSgenome MEDIPS • 748 views
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