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Question: cn.mops error - Help !
1
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Hi all,

I am using cn.mops Bioconductor package for analysis of CNV in exome-seq data. But whever I run referencecn.mops, the program throws an error:

Error in strand(input) : error in evaluating the argument 'x' in selecting a method for function 'strand': Error: object 'input' not found

I tried changing strand information manually, created GRanges object manually , but nothing works. But, if I use the same GRanges object with the function cn.mops - it works flawlessly without any error.

Any help is appreciated.

edit: My Command -

aml.cn.ref=referencecn.mops(cases=aml.counts[,2:3],controls=aml.counts[,1],parallel=4,segAlgorithm="DNAcopy")

where, aml.counts is a GRanges object with 3 meta data column representing the read counts for bait regions. 1st meta data column is for control where 2nd and 3rd are for tumor. I have also tried with single case (tumor), but it gives me the same error.

Thank you.

ADD COMMENTlink 5.8 years ago poisonAlien ♦ 2.8k • updated 5.7 years ago Biostar 20
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1

What is the exact command that you're issuing? The error indicates that you're just not calling the function correctly.

ADD REPLYlink 5.8 years ago
Devon Ryan
90k
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Hi Devon,

Thank you. I have edited my question with the command. Other arguments were left for default.

ADD REPLYlink 5.8 years ago
poisonAlien
♦ 2.8k
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Do strand(IRanges::sort(aml.counts[,2:3])) and strand(IRanges::sort(aml.counts[,1])) produce the same error? Also, what's the output of sessionInfo()? I'm not entirely sure how this error should even be possible from looking at the code.

ADD REPLYlink 5.8 years ago
Devon Ryan
90k
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Hi Devon,

Those commands did not produce any sorta error. Its very confusing now, the same object can be run be run with normal cn.mops but fails with referencecn.mops. However, my sessionInfo() is as below.

> sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-pc-linux-gnu (64-bit)

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_SG.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_SG.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_SG.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] parallel stats graphics grDevices utils datasets methods base

other attached packages: [1] DNAcopy_1.34.0 BiocInstaller_1.10.4 snow_0.3-13 cn.mops_1.6.7 GenomicRanges_1.12.5 IRanges_1.18.4 [7] Biobase_2.20.1 BiocGenerics_0.6.0

loaded via a namespace (and not attached): [1] Biostrings_2.28.0 bitops_1.0-6 Rsamtools_1.12.4 stats4_3.0.1 tools_3.0.1 zlibbioc_1.6.0

ADD REPLYlink 5.8 years ago
poisonAlien
♦ 2.8k
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2

Yup ! Did the trick. I was still using a year old bioC (so dumb of me). Updated both R and bioC with new version, now its working !!

Thank you :)

ADD REPLYlink 5.8 years ago
poisonAlien
♦ 2.8k

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