saint

Documentation

Overview

Package saint reads and parses SAINT-related files.

Index

• type BaitDatRow
  • func BaitDat(filename string) []BaitDatRow
• type InterDatRow
  • func InterDat(filename string) []InterDatRow
• type PreyDatRow
  • func PreyDat(filename string) []PreyDatRow
• type Row
• type SAINT
  • func Read(filename string, fdr float64, minBaits int) *SAINT
  • func (saint *SAINT) FilterByBaitNumber(minimumBaits int)
  • func (s *SAINT) FilterByFDR(fdr float64)
  • func (s *SAINT) GetUniProtMapping() map[string]string
  • func (s *SAINT) LengthNormalizeSpectralCounts()
  • func (s *SAINT) ParseInteractors(fdr float64) map[string][]string
  • func (s *SAINT) SortByPreyRank(field string) map[string][]string

Types

type BaitDatRow

type BaitDatRow struct {
	ID      string
	Name    string
	Control bool
	Type    string // This is for an optional 4th column that I can add to the file.
}

BaitDatRow defines the headers in a bait.dat file.

func BaitDat

func BaitDat(filename string) []BaitDatRow

BaitDat reads a bait.dat file.

type InterDatRow

type InterDatRow struct {
	ID   string
	Bait string
	Prey string
	Spec int
}

InterDatRow defines the headers in a bait.dat file.

func InterDat

func InterDat(filename string) []InterDatRow

InterDat reads a prey.dat file.

type PreyDatRow

type PreyDatRow struct {
	Accession string
	Length    int
	Name      string
}

PreyDatRow defines the headers in a bait.dat file.

func PreyDat

func PreyDat(filename string) []PreyDatRow

PreyDat reads a prey.dat file.

type Row

type Row struct {
	Bait               string
	Prey               string
	PreyGene           string
	Spec               []float64
	AvgSpec            float64
	Control            []float64
	AvgP               float64
	FoldChange         float64
	FDR                float64
	NormalizedSpec     float64
	PreySequenceLength int
}

Row defines the headers in a SAINT file.

type SAINT

type SAINT []Row

SAINT is an array of Rows from a SAINT file.

func Read

func Read(filename string, fdr float64, minBaits int) *SAINT

Read reads a SAINT file and filters by FDR.

func (*SAINT) FilterByBaitNumber

func (saint *SAINT) FilterByBaitNumber(minimumBaits int)

FilterByBaitNumber filters a SAINT file by a minimum bait number required per prey.

func (*SAINT) FilterByFDR

func (s *SAINT) FilterByFDR(fdr float64)

FilterByFDR removes preys not passing an FDR.

func (*SAINT) GetUniProtMapping

func (s *SAINT) GetUniProtMapping() map[string]string

GetUniProtMapping creates a map from UniProt accessions to gene names using the Refseq "Prey" column IDs.

func (*SAINT) LengthNormalizeSpectralCounts

func (s *SAINT) LengthNormalizeSpectralCounts()

LengthNormalizeSpectralCounts substracts control counts from the average spectral count and then multiplies by the median prey length for the bait / current prey length.

func (*SAINT) ParseInteractors

func (s *SAINT) ParseInteractors(fdr float64) map[string][]string

ParseInteractors returns significant interactors for each bait.

func (*SAINT) SortByPreyRank

func (s *SAINT) SortByPreyRank(field string) map[string][]string

SortByPreyRank returns a list of preys for each bait, sorted in order of the spectral count or normalized spectral count