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https://github.com/broadinstitute/getzlab-pcawg-pvalue_combination

p value combination for PCAWG drivers

https://github.com/broadinstitute/getzlab-pcawg-pvalue_combination

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p value combination for PCAWG drivers

Basic Info
  • Host: GitHub
  • Owner: broadinstitute
  • License: bsd-3-clause
  • Language: R
  • Default Branch: master
  • Size: 6.34 MB
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Created almost 7 years ago · Last pushed over 6 years ago
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README.md

getzlab-pvalue_combination

p-value combination for PCAWG drivers

Note: we are using parts of the original code for the Empirical Brown's method (Poole et al. Bioinformatics, 2016). For details, check the following github repo: https://github.com/IlyaLab/CombiningDependentPvaluesUsingEBM

Requirements: R-3.4, uses package reshape.

The inputs to the R script are: tissue, target, dir, siffilepath. The outputs contain a a diagnostic QQ plot of observed vs. expected p-values for all input p-value sets, a table with combined p-values, a report that indicates which p-value sets were included and a table of combined p-values after removing some outlier methods (.combinedpvalues.automaticmethod_removal.txt). For details please see Rheinbay, Nielsen, Abascal, Wala, Shapira et al.

Steps:

  1. Copy ebm.R from https://github.com/IlyaLab/CombiningDependentPvaluesUsingEBM into pvalue_combination/

  2. Unarchive exampledata/PCAWGmetaCarcinomacds_pvalues.zip

  3. Run the following command to integrate p values for Carcinoma CDS (protein-coding) regions:

Rscript pvaluecombination/runpvaluecombinationcomparisonautomaticremoval.R metaCarcinoma CDS output/ exampledata/SIF_input.txt

All results are saved under output/

Columns in .automaticmethodremoval_report.txt:

siggenecounts: number of significant genes (q<0.1) called by the respective method

median_sig: median number of significant genes across all methods

upper_thresh: upper threshold (gene count) to call a method inflated

removedforinflation: 0 not removed, 1 removed for inflation

Owner

  • Name: Broad Institute
  • Login: broadinstitute
  • Kind: organization
  • Location: Cambridge, MA

Broad Institute of MIT and Harvard

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