CNRegions gives error in IRanges Package
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@sumonaray55-16026
Last seen 4.2 years ago

I am handling CNV data. While running CNregions function for iClusterPlus the way they have shown here (https://www.mskcc.org/sites/default/files/node/18547/documents/iclusterplususerguide_0.pdf):

cnv_seg=read.table(file="~/Desktop/iCluster_Plus_files/CNV.txt",header=T)
> cnv=CNregions(seg = cnv_seg, epsilon = 0, adaptive = FALSE, rmCNV = TRUE, cnv = variation.hg18.v10.nov.2010, frac.overlap = 0.5, rmSmallseg = TRUE, nProbes = 5)
Removing CNV...
Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") :
solving row 1: negative widths are not allowed

I have checked that the width are non-negative. The same error is coming even if I am using the gbm.seg data (a subset of the glioblastoma dataset from the cancer genome atlas (TCGA) GBM study (2009) used in Shen et al. (2012 ), available in R).

How to solve?

CNregions iranges iClusterPlus • 514 views
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You need to provide a self-contained example data set that gives the error, which people can use to track down any problems. The IRanges package is pretty mature, and thousands of people have used it without problems, so it is more likely that you misunderstand the error rather than there being a bug in IRanges.