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Rafael Barrero Rodríguez
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Oct 27, 2023
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@echo off | ||
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rem Initialize the variable for the argument | ||
set "config=" | ||
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rem Check if an argument was provided | ||
if not "%~1"=="" ( | ||
set "config=%~1" | ||
echo Configuration file path: %~1 | ||
) else ( | ||
echo Configuration file was not provided. | ||
exit /b 1 | ||
) | ||
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for %%I in ("%~dp0") do set "base_path=%%~fI" | ||
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set "Rexe_relative=R-Portable\App\R-Portable\bin\x64\Rscript.exe" | ||
set "Rexe_path=%base_path%%Rexe_relative%" | ||
set "Rscript=%base_path%R-Portable/app_wo_GUI.R" | ||
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echo Executing command: "%Rexe_path%" "--vanilla %Rscript% %config%" | ||
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"%Rexe_path%" "--vanilla %Rscript% %config%" |
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report_infile: D:\ReportAnalysis\2_ReportLimma_wo_GUI\test\test1\NM_qfq_table_pgmfreq.tsv | ||
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sample_table: D:\ReportAnalysis\2_ReportLimma_wo_GUI\limma_sample_table.tsv | ||
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outfile: D:\ReportAnalysis\2_ReportLimma_wo_GUI\test\test1\LIMMA_NM_qfq_table_pgmfreq.tsv | ||
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# Possible types | ||
# - limma | ||
# - limma_with_duplicates | ||
# - t-test | ||
test_type: | ||
- limma | ||
- limma_with_duplicates | ||
- t-test | ||
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integrations: | ||
- Z_pgm2p | ||
- Z_pgm2p_dNM | ||
- Z_p2qf | ||
- Z_qf2qfq | ||
- Z_qfq2qfqall | ||
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hypothesis_testing: | ||
- [ H, C ] | ||
- [ Control, Heteroplasmy ] |
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C H Control Heteroplasmy | ||
C1 H1 C1 H1 | ||
C2 H2 C2 H2 | ||
C3 H3 C3 H3 | ||
H4 H4 |
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