Support Modules: panoply_harmonize

panoply_harmonize

Description

This module harmonizes RNA, CNA, and proteome data to create gene-centric tables with common samples as columns and common genes as rows.

Input

Required inputs:

• inputData: (.tar file) tarball from panoply_rna_protein_correlation
• rnaExpr: (.gct file) RNA expression data
• cnaExpr: (.gct file) CNA expression data
• type: (String) data type
• standalone: (String)
• yaml: (.yaml file) master-parameters.yaml

Optional inputs:

• analysisDir: (String) name of analysis directory
• pomeGeneIdCol: (String, default = 'GeneSymbol') gene id column in proteome data
• cnaGeneIdCol: (String, default = 'id') gene id column in CNA expression data
• rnaGeneIdCol: (String, default = 'id') gene id column in RNA expression data
• na_max: (Float, default = 0.7) maximum allowed NA values per protein/site/row; can be fraction.
• duplicate_gene_policy: (String, default = 'maxvar')
• gene_id_col: (String, default = 'geneSymbol') name of sample annotation column containing gene ids.
• outFile: (String, default = "panoply_harmonize-output.tar") output .tar file name

Output

• outputs Tarball including the following files in the harmonized-data subdirectory:
  • Harmonized data matrices for CNA (cna-matrix.csv), RNA (rna-matrix.csv) and proteome (*-matrix.csv) with samples (columns) and genes (rows) in identical order in all tables.
  • Matching sample annotation for samples included in the data matrices (sample-info.csv)
  • Class vectors files (*.cls) for all sample annotations