types

Documentation

Overview

Package types contains type definitions used throughout pep2gene

Index

• type Gene
  • func (g Gene) Copy() *Gene
• type Genes
• type Parameters
• type Peptide
• type PeptideStat
  • func (p PeptideStat) Copy() *PeptideStat
• type Peptides
• type Protein

Types

type Gene

type Gene struct {
	Count        float64
	IsSubsumed   bool
	PeptideCount map[string]float64
	Peptides     []string
	Shared       []string
	Subsumed     []string
	Unique       float64
	UniqueShared int
}

Gene contains based information: 1) is the gene subsumed by another, 2) The (modified) peptides that match to it and their spectral counts, 3) the peptides that match to it to, 4) any genes that it completely shares its peptides with, 5) the spectral count, 6) any genes it subsumes, 7) the number of unique peptides it has (used for distributing spectral counts, so this can be a decimal for genes that share peptides), 8) the number of unique peptides shared between genes that perfectly share their peptides

func (Gene) Copy

func (g Gene) Copy() *Gene

Copy will copy a Gene to a new pointer

type Genes

type Genes map[string]*Gene

Genes is a map of gene IDS to their peptide and gene info

type Parameters

type Parameters struct {
	Database                    string
	Enzyme                      string
	FDR                         float64
	File                        string
	IgnoreDecoys                bool
	IgnoreInvalid               bool
	InferEnzyme                 bool
	MapFile                     string
	MissedCleavages             int
	Mscore                      float64
	MscorePeptideExperimentWide float64
	OutFormat                   string
	PeakGroupRank               int
	PeptideProbability          float64
	Pipeline                    string
}

Parameters for command line arguments.

type Peptide

type Peptide struct {
	Modified  string
	Intensity float64
	Sequence  string
}

Peptide contains the amino acid "Sequence" for a peptide and the "Modified" version, and the intensity when using intensity based data (e.g. OpenSwath)

type PeptideStat

type PeptideStat struct {
	Count    float64
	Genes    []string
	Modified map[string]float64
	Unique   bool
}

PeptideStat contains the spectral count for a peptide and the individual counts for its modified forms

func (PeptideStat) Copy

func (p PeptideStat) Copy() *PeptideStat

Copy will copy a PeptideStat to a new pointer

type Peptides

type Peptides map[string]*PeptideStat

Peptides is a map of peptides to their spectral counts and modified forms

type Protein

type Protein struct {
	GeneID          string
	GeneName        string
	MatchedPeptides []string
	Sequence        string
	Valid           bool
}

Protein contains the protein name, gene ID and sequence for a protein