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
	InferEnzyme        bool
	MapFile            string
	MissedCleavages    int
	OutFormat          string
	PeptideProbability float64
	Pipeline           string
}

Parameters for command line arguments.

type Peptide

type Peptide struct {
	Modified string
	Sequence string
}

Peptide contains the amino acid "Sequence" for a peptide and the "Modified" version.

type PeptideStat

type PeptideStat struct {
	Count    int
	Genes    []string
	Modified map[string]int
	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
}

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