How to run MutSigCV example correctly
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Entering edit mode
4.9 years ago
ShirleyDai ▴ 40

Hi, I am trying to run MutsigCV as indicated by enter link description here. Does someone have some ideas? Thanks

The command is:

MutSigCV('LUSC.mutations.maf','exome_full192.coverage.txt','gene.covariates.txt','my_results','mutation_type_dictionary_file.txt','chr_files_hg19')

But got the error messages:

MutSigCV: PREPROCESS
--------------------
Loading mutation_file...
Loading coverage file...
Out of memory. Type HELP MEMORY for your options.

Error in MutSigCV>text_to_lines (line 2183)
    if X(end)==10, X(end)=[];   % remove trailing blank lines

Error in MutSigCV>load_lines (line 1367)
  L = text_to_lines(X);

Error in MutSigCV>load_struct (line 1486)
    q = load_lines(args{1});

Error in MutSigCV>load_struct_specify_string_cols (line 1569)
  X = load_struct(fname,format,char(9),num_header_lines,P);

Error in MutSigCV>MutSig_preprocess (line 251)
  C = load_struct_specify_string_cols(coverage_file,1:3); % gene effect categ are all strings

Error in MutSigCV (line 184)
  MutSig_preprocess(mutation_file,coverage_file,covariate_file,output_filestem,varargin{:})
musigcv • 2.3k views
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