Data Preparation Modules: panoply_preprocess_gct

panoply_preprocess_gct

Description

This module collapses a feature-level GCT to a gene-centric (for ssGSEA) or site-centric (for PTM-SEA) level, as an appropriate input GCT for the panoply_ssgsea module.

Input

Required inputs:

• input_ds: (.gct file) input GCT file
• yaml_file: (.yaml file) master-parameters.yaml
• output_prefix: (String) File prefix for output files.

Optional inputs:

• acc_type: (String) Type of accession number in 'rid' object in GCT file ("uniprot", "refseq" (default), "symbol").
• id_type: (String) Notation of site-ids: 'sm' - Spectrum Mill (default); 'wg' - Web Gestalt; 'ph' - Philosopher. Only relevant for PTM-SEA.
• id_type_out (String) Type of site id for output: 'uniprot'(default), 'refseq', 'seqwin'. Only relevant for PTM-SEA.
• level (String) Mode of report:
  • 'ssc' - single-site-centric
  • 'gc' - gene-centric (default)
  • 'gcr' - gene-centric-redundant
• loc (Boolean) If TRUE only fully localized sites will be considered (default: TRUE). Localization infromation is expected to be encoded in the site identifier. Respective parsing rules are determined by '--id_type'.
• gene_col: (String) Name of column listing gene names; used for gene centric reports (default: "geneSymbol").
• humanize_gene: (Boolean) If TRUE, gene symbols will be capitalized; can be used to crudely humanize mouse or rat gene symbols.
• seqwin_col: (String) "Column containing flanking sequences, separated by '|'. Only relevant for PTM-SEA and if '--id_type_out' = 'seqwin' (default: 'VMsiteFlanks').
• SGT_col: (String) Column used to collpase subgroup-top (SGT) reports (default: "subgroupNum). Only relevant for Spectrum Mill protein reports.
• mod_res: (String) Modified residues, e.g. "S|T|Y" or "K" (default: "S|T|Y").
• mod_type: (String) Type of post-translational modification, e.g "p" for phospho (default) or "ac" for acetylation
• mode: (String) Determines how multiple features (e.g. proteins, PTM sites, etc.) mapping to the same gene symbol will be aggregated:
  • "mean" - mean
  • "median" - median
  • "sd - most variable (standard deviation) across sample columns
  • "SGT" - subgroup top: first subgroup in protein group (Spectrum Mill)
  • "abs.max" - for log-transformed, signed p-values"

Output

• result: (.gct file) Preprocessed GCT file, appropriate for use in ssGSEA or PTM-SEA