cn.mops error - Help !

Question

[poisonAlien]

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.

[Devon Ryan]

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

[poisonAlien]

Hi Devon,

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

[Devon Ryan]

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.

[poisonAlien]

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

[poisonAlien]

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 :)