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) MATLAB:UndefinedFunction
I have installed OncoSNP from this site and corresponding MCR library(R2013b) installer too.
Thanks in advance