Question: BICseq R package problem
1
gravatar for Nicola Casiraghi
3.3 years ago by
Trento, IT
Nicola Casiraghi420 wrote:

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

R cnv bicseq wgs • 2.4k views
ADD COMMENTlink modified 7 months ago by Biostar ♦♦ 20 • written 3.3 years ago by Nicola Casiraghi420
3

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!

 

ADD REPLYlink written 2.2 years ago by richard.deborja90
1

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.  

ADD REPLYlink written 2.2 years ago by alan70
1

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

ADD REPLYlink written 2.2 years ago by Danielk530
2
gravatar for Danielk
3.0 years ago by
Danielk530
Karolinska Institutet, Stockholm, Sweden
Danielk530 wrote:

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

ADD COMMENTlink written 3.0 years ago by Danielk530
1
gravatar for Kizuna
3.3 years ago by
Kizuna720
France, Paris
Kizuna720 wrote:

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

ADD COMMENTlink written 3.3 years ago by Kizuna720

Hi Kiz,

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

ADD REPLYlink written 3.3 years ago by Nicola Casiraghi420
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1449 users visited in the last hour