Question: oncoSNP stops run giving MATLAB function error
gravatar for SJ Basu
9 months ago by
SJ Basu30
SJ Basu30 wrote:

Hello everyone,

Hope this message find everyone in good health.

Our lab has generated SNP array data of tumor samples using Illumina CytoSNP 850K beadchip array. Now I am trying to to set up a pipeline to analyze the data and after reading through a few papers, found PennCNV and QuantiSNP/OncoSNP to be popular tools. So I extracted the LRR values from the the data files using bedtools plugins and illumina's EGT normalization files. now the data looks like this:

SNP Name        Chr     Position        Log R Ratio     B Allele Freq
rs4477212       chr1    82154   0.314346        0.00559425
rs3131972       chr1    752721  -0.270539       0.514414
rs12562034      chr1    768448  -0.305087       0.942383
rs12124819      chr1    776546  0.925362        0.00254118

This was given as input to OncoSNP v1.4 (2014). The tool then starts running then stops mid-way giving the following error:

OncoSNP v1.4 (2014). Internal version v3.1
OncoSNP: Performing unpaired tumour sample analysis.
OncoSNP: Running in single sample analysis mode.
OncoSNP: Reading: /home/sangramjit/Desktop/SNParray_analysis/oncosnp_output/txt_4m_gtc/204240030107_R08C01.txt
OncoSNP: Doing GC content correction: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 
Warning: Window size must be less or equal as the number of elements.
> In nanmoving_average at 83
  In initialiseModelParams at 36
  In oncosnp_main at 42
  In oncosnp at 506 
OncoSNP: Loading system options ...
OncoSNP: EM Iteration: 1
Undefined function or variable "loglik".

Error in calcLikelihoodQuick (line 298)

Error in runEMQuick (line 23)

Error in oncosnp_main (line 59)

Error in oncosnp (line 506)


I have installed OncoSNP from this site and corresponding MCR library(R2013b) installer too.

Please help.

Thanks in advance

snp matlab oncosnp snp-array array • 173 views
ADD COMMENTlink written 9 months ago by SJ Basu30
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