WIFA-X Identification of cancer-driver genes in focal genomic aberrations from whole exome sequencing data


You can start WIFA-X analysis from your own log2 copy number input instead of using provided 'quantify_copy_number_aberration.r' code. If you want to use normalized log2 ratio signal from EXCAVATOR2 program, use 'copy_number_aberration_from_EXCAVATOR2.r' code.

Shell>copy_number_aberration_from_EXCAVATOR2.r <SAMPLE FILE LIST> <DIR OUTPUT> <NUM PROCESSES>

  • SAMPLE FILE LIST : The file path of the table containing unique sample identifiers and path of HSLMResults from EXCAVATOR2 program
  • DIR OUTPUT : The path of output file directory
  • NUM PROCESSES : The number of clusters to process concurrently
Here's an example list of SAMPLE FILE LIST

id path
S003 /home/tom/ExperimentalFileAnalysis/Results/sample3/HSLMResults_sample3.txt
S009 /home/tom/ExperimentalFileAnalysis/Results/sample9/HSLMResults_sample9.txt
S015 /home/tom/ExperimentalFileAnalysis/Results/sample15/HSLMResults_sample15.txt
S029 /home/tom/ExperimentalFileAnalysis/Results/sample20/HSLMResults_sample29.txt

After generating log2 copy number file using 'copy_number_aberration_from_EXCAVATOR2.r', you can run the remaining steps from 'identify_focal_aberrations.r'. Please refer to the manual pdf file.