pcquant Module

roll_up

proteoclade.pcquant.roll_up(file, unique_taxon='species', inclusion_list=None, exclusion_list=None, samples='implicit', default_taxon=None, missing_values=True)

Roll up peptides to the gene level, producing gene- and taxon specific outputs.

Parameters

  • file (string) – .csv or tab .txt input file to roll peptides up to genes

  • unique_taxon (string) – Taxon level which is used to determine uniqueness and identity (default “species”). Please check the ncbi_ranks global variable for valid ranks, or use “organisms”, after annotating with annotate_peptides or annotate_denovo.

  • inclusion_list (None or tuple) – Taxon members that must be matched for a peptide to be included, if specified (default None)

  • exclusion_list (None or tuple) – Taxon members that must NOT be matched for a peptide to be included, if specified (default None)

  • samples (string) – Method to use for finding samples in file, either “implicit” or “explicit” (default “implicit”)

  • default_taxon (None or string) – Member of a taxonomy that will be assigned identity even if the peptide is shared with different members of the same taxonomic level (default None)

  • missing_values (bool) – When adding samples, decide whether to include a gene if any samples have 0 or NaN in their quantitation (default True)

Examples

>>> roll_up("annotated_denovo_matched_experiment.txt") # species-specific gene rollup

Notes

Output is .csv or .txt file with unique taxon, unique genes, and samples