Main pyGenClean pipeline

Here is the usage of the main pipeline.

$ run_pyGenClean --help
usage: run_pyGenClean [-h] [-v] [--bfile FILE] [--tfile FILE] [--file FILE]
                      [--report-title TITLE] [--report-author AUTHOR]
                      [--report-number NUMBER]
                      [--report-background BACKGROUND] --conf FILE

Runs the data clean up (pyGenClean version 1.8.3).

optional arguments:
  -h, --help            show this help message and exit
  -v, --version         show program's version number and exit

Input File:
  --bfile FILE          The input file prefix (will find the plink binary
                        files by appending the prefix to the .bim, .bed and
                        .fam files, respectively).
  --tfile FILE          The input file prefix (will find the plink transposed
                        files by appending the prefix to the .tped and .tfam
                        files, respectively).
  --file FILE           The input file prefix (will find the plink files by
                        appending the prefix to the .ped and .fam files).

Report Options:
  --report-title TITLE  The report title. [default: Genetic Data Clean Up]
  --report-author AUTHOR
                        The current project number. [default: pyGenClean]
  --report-number NUMBER
                        The current project author. [default: Simple Project]
  --report-background BACKGROUND
                        Text of file containing the background section of the
                        report.

Configuration File:
  --conf FILE           The parameter file for the data clean up.

Algorithm

For more information about the algorithms, have a look below.

• pyGenClean package
  • Subpackages
    • pyGenClean.Contamination package
      • Module contents
      • Submodules
    • pyGenClean.DupSNPs package
      • Module contents
      • Submodules
    • pyGenClean.DupSamples package
      • Module contents
      • Submodules
    • pyGenClean.Ethnicity package
      • Module contents
      • Submodules
    • pyGenClean.FlagHW package
      • Module contents
      • Submodules
    • pyGenClean.FlagMAF package
      • Module contents
      • Submodules
    • pyGenClean.HeteroHap package
      • Module contents
      • Submodules
    • pyGenClean.LaTeX package
      • Submodules
      • pyGenClean.LaTeX.auto_report module
      • pyGenClean.LaTeX.merge_reports module
      • pyGenClean.LaTeX.utils module
      • Module contents
    • pyGenClean.MarkerMissingness package
      • Module contents
      • Submodules
    • pyGenClean.Misc package
      • Submodules
      • pyGenClean.Misc.compare_gold_standard module
      • Module contents
    • pyGenClean.NoCallHetero package
      • Module contents
      • Submodules
    • pyGenClean.PlateBias package
      • Module contents
      • Submodules
    • pyGenClean.PlinkUtils package
      • Module contents
      • Submodules
    • pyGenClean.RelatedSamples package
      • Module contents
      • Submodules
    • pyGenClean.SampleMissingness package
      • Module contents
      • Submodules
    • pyGenClean.SexCheck package
      • Module contents
      • Submodules
  • Submodules
  • pyGenClean.pipeline_error module
  • pyGenClean.run_data_clean_up module
  • pyGenClean.version module
  • Module contents