ExomeCopy package error
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Hi, I am testing ExomeCopy on a set of illumina sequencing data generated after agilent custum gene set capture, only 35 gene exons overall (~ 300 Mb total). 1-My first question would be : is the method reliable for smaller capture? 2-Secondly., I sucessfully used the method on the data provided with the vignette. I then tried with my own set of data in total 10 samples, across 2282 rows , I have calculated the GC and bg values nad went on to the next step where I ran exomeCopy on one sample and one chromosome ###this seems to work for certains samples, expect the warning for small subset > fit <- exomeCopy(rdata["Chr10"], sample.name = exome.samples[10], + X.names = c("bg", "GC", "GC.sq", "width"), S = 0:6, + d = 2) Warning message: In exomeCopy(rdata["Chr10"], sample.name = exome.samples[10], X.names = c("bg", : exomeCopy was tested for thousands of ranges covering a targeted region on a single chromosome. The results might not be reliable for less than a hundred ranges. ###then I try with another sample and got this error message Error in if (goto.cnv < 1/(nstates - 1)) { : missing value where TRUE/FALSE needed I am not sure where this comes from and would like some help on this > fit <- exomeCopy(rdata["Chr10"], sample.name = exome.samples[7], + X.names = c("bg", "GC", "GC.sq", "width"), S = 0:6, + d = 2) Error in if (goto.cnv < 1/(nstates - 1)) { : missing value where TRUE/FALSE needed In addition: Warning message: In exomeCopy(rdata["Chr10"], sample.name = exome.samples[7], X.names = c("bg", : exomeCopy was tested for thousands of ranges covering a targeted region on a single chromosome. The results might not be reliable for less than a hundred ranges. > exome.samples [1] "sample9" "sample8" "sample7" "sample6" "sample5" "sample1" [7] "sample16" "sample15" "sample14" "sample13" example if my data ##### RangedData with 2282 rows and 15 value columns across 18 spaces space ranges | sample9 sample8 sample7 <factor> <iranges> | <integer> <integer> <integer> 1 Chr1 [115247069, 115247168] | 4369 4446 3675 2 Chr1 [115247169, 115247268] | 8222 8081 6978 3 Chr1 [115247269, 115247368] | 9548 10026 8690 -- output of sessionInfo(): R version 2.15.0 (2012-03-30) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=C [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] exomeCopy_1.2.0 Rsamtools_1.8.6 Biostrings_2.24.1 [4] GenomicRanges_1.8.13 IRanges_1.14.4 BiocGenerics_0.2.0 loaded via a namespace (and not attached): [1] bitops_1.0-4.1 stats4_2.15.0 tools_2.15.0 zlibbioc_1.2.0 -- Sent via the guest posting facility at bioconductor.org.
Sequencing exomeCopy Sequencing exomeCopy • 691 views
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