BICseq R package problem

Question

[Nicola Casiraghi]

Hi all,

I am interested in using the tool BICseq for a CNV detection analysis. Unfortunately, I am writing you because I cannot solve a problem related to BICseq R package.

The R package is correctly installed and I am testing it on chr22 extracted from a in home BAM file. Running the function getBICseg with default parameters and a correctly generated bicseq object using the BICseq function, the following error is reported:

Error in .C("sort_rms_binning", as.integer(sample), length(sample), as.integer(reference),  : "sort_rms_binning" not resolved from current namespace (BICseq)"

Please, could you help me fixing the problem?

I am using the R version 3.0.1.

I found other posts related to this problem here but no answers.

Many thanks in advance!

Nicola

[richard.deborja]

There's been an update to the way C libraries are handled with R 3.0.x. You'll need to untar the R package and edit the NAMESPACE file to include the following line:

useDynLib(BICseq)

Save the file and run R CMD check BICseq then R CMD INSTALL BICseq (note the use of the unpacked directory name instead of the tar.gz file). Hope this helps!

[alan]

Please add this as a solution rather than a comment. We've been looking for an answer to this issue for literally months, but have instead been hanging on to a 2.15.x copy of R.

[Danielk]

We've stopped using it completely because of this issue.

Answer 1

[Danielk]

I've only been able to install and run BICseq on R-2.15.1.

You can also check out the following packages (in BioC)

• QDNAseq
• CNAnorm

Answer 2

[Kizuna]

Hi Nicola,

I use ExomeDepth for CNV detection which works really well on R 3.0.2.. If you think that this library might be useful for your analysis, I may be able to help .

Kiz

[Nicola Casiraghi]

Hi Kiz,

thank you for the suggestion, however I need tool for WGS data analysis.