ExomeCopy error
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Kevin Lee ▴ 40
@kevin-lee-5904
Last seen 6.6 years ago
Hello, I am working with ExomeCopy, and I cannot get past this error: fit.list <- lapply(sample.names, runExomeCopy, seqs) *Error in negLogLike(c(logit(goto.cnv), logit(goto.normal), beta.hat, log(phi.hat)), :* * NA/NaN/Inf in foreign function call (arg 5)* where: runExomeCopy <- functionsample.name, seqs) { lapply(seqs, functionseq.name) exomeCopy(counts[seq.name], sample.name, X.names = c("log.bg", "GC", "GC.sq", "width"), S = 0:4, d = 2)) } (I have followed the vignette as closely as possible.) There are some exons that have zero reads for all 7 samples. Could this be causing the error? And if so, how can I remove these rows (ranges) from the counts RangeData object? Cheers, Kevin -- Kevin Lee Georgia Institute of Technology Department of Biology PhD candidate in Bioinformatics [[alternative HTML version deleted]]
exomeCopy exomeCopy • 866 views
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@mikelove
Last seen 9 minutes ago
United States
hi Kevin, It could be the rows with zero coverage. I have an example of removing rows with zero coverage in the third code chunk of section 3.5 of the vignette. Mike On Mon, Apr 29, 2013 at 9:32 PM, Kevin Lee <kevinjosephlee@gmail.com> wrote: > Hello, > > I am working with ExomeCopy, and I cannot get past this error: > > fit.list <- lapply(sample.names, runExomeCopy, seqs) > *Error in negLogLike(c(logit(goto.cnv), logit(goto.normal), beta.hat, > log(phi.hat)), :* > * NA/NaN/Inf in foreign function call (arg 5)* > > where: > runExomeCopy <- functionsample.name, seqs) { lapply(seqs, function( > seq.name) > exomeCopy(counts[seq.name], sample.name, X.names = c("log.bg", "GC", > "GC.sq", "width"), S = 0:4, d = 2)) } > > (I have followed the vignette as closely as possible.) > > > There are some exons that have zero reads for all 7 samples. Could this be > causing the error? And if so, how can I remove these rows (ranges) from > the counts RangeData object? > > > Cheers, > > Kevin > > > -- > Kevin Lee > Georgia Institute of Technology > Department of Biology > PhD candidate in Bioinformatics > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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Thanks Mike, I have now run exomeCopy to completion. Unfortunately, the output looks erroneous. The percent normal state is very low for all of the samples (around 10%). And consequently, when I visualize the plots using: cnv.cols <- c("red", "orange", "black", "deepskyblue", "blue") plotCompiledCNV(CNV.segments = CNV.segments, seq.name = "1", col = cnv.cols) plotCompiledCNV(CNV.segments = CNV.segments, seq.name = "2", col = cnv.cols) plotCompiledCNV(CNV.segments = CNV.segments, seq.name = "3", col = cnv.cols) plotCompiledCNV(CNV.segments = CNV.segments, seq.name = "4", col = cnv.cols) etc, most plots for all of the individuals are orange. I presume that there should be no color if compiled.segments$copy.count == 2 because I removed them as the vignette suggested: CNV.segments <- compiled.segments[compiled.segments$copy.count != 2, ] A few of the model parameters are as follows: > fit.list[[1]][[1]]@init.par$beta.hat intercept log.bg GC GC.sq width 137.73955 227.35661 -185.97921 219.07224 -1.41302 > fit.list[[1]][[1]]@final.par$beta intercept log.bg GC GC.sq width 287.284313 187.588809 -206.468309 214.974768 -1.189761 > fit.list[[1]][[2]]@init.par$beta.hat intercept log.bg GC GC.sq width 168.7144028 220.0425351 -195.0044913 210.9412808 -0.2804571 > fit.list[[1]][[2]]@final.par$beta intercept log.bg GC GC.sq width 284.3057111 153.1812321 -204.5005754 217.3399872 0.3090188 > fit.list[[2]][[2]]@init.par$beta.hat intercept log.bg GC GC.sq width 183.6010329 239.9594618 -215.7970168 229.9454217 -0.3597293 > fit.list[[2]][[2]]@final.par$beta intercept log.bg GC GC.sq width 252.8972821 131.2518196 -253.0415091 241.4809859 -0.8693721 I see that these parameters are far off from those present in the vignette. Is this the problem? btw - I am using a sorted bed file of CCDS as the input bed; I presumed that these are not overlapping. And at any rate, I didn't suspect that this was the issue. Any reason why exomeCopy is not "seeing" d=2 as the expected value? Cheers, Kevin On Mon, Apr 29, 2013 at 5:37 PM, Michael Love <michaelisaiahlove@gmail.com>wrote: > hi Kevin, > > It could be the rows with zero coverage. I have an example of removing > rows with zero coverage in the third code chunk of section 3.5 of the > vignette. > > Mike > > > > On Mon, Apr 29, 2013 at 9:32 PM, Kevin Lee <kevinjosephlee@gmail.com>wrote: > >> Hello, >> >> I am working with ExomeCopy, and I cannot get past this error: >> >> fit.list <- lapply(sample.names, runExomeCopy, seqs) >> *Error in negLogLike(c(logit(goto.cnv), logit(goto.normal), beta.hat, >> log(phi.hat)), :* >> * NA/NaN/Inf in foreign function call (arg 5)* >> >> >> where: >> runExomeCopy <- functionsample.name, seqs) { lapply(seqs, function( >> seq.name) >> exomeCopy(counts[seq.name], sample.name, X.names = c("log.bg", "GC", >> "GC.sq", "width"), S = 0:4, d = 2)) } >> >> (I have followed the vignette as closely as possible.) >> >> >> There are some exons that have zero reads for all 7 samples. Could this >> be >> causing the error? And if so, how can I remove these rows (ranges) from >> the counts RangeData object? >> >> >> Cheers, >> >> Kevin >> >> >> -- >> Kevin Lee >> Georgia Institute of Technology >> Department of Biology >> PhD candidate in Bioinformatics >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > -- Kevin Lee Georgia Institute of Technology Department of Biology PhD candidate in Bioinformatics [[alternative HTML version deleted]]