pwm

Documentation

Overview

Package pwm implements a position weight matrix search based on an algorithm by Deborah Toledo Flores.

Index

• type Feature
  • func (f *Feature) Description() string
  • func (f *Feature) End() int
  • func (f *Feature) Len() int
  • func (f *Feature) Location() feat.Feature
  • func (f *Feature) MolType() feat.Moltype
  • func (f *Feature) Name() string
  • func (f *Feature) Orientation() feat.Orientation
  • func (f *Feature) Start() int
• type PWM
  • func New(matrix [][]float64) (m *PWM)
  • func (m *PWM) Search(s Sequence, start, end int, minScore float64) []feat.Feature
• type Sequence

Types

type Feature

type Feature struct {
	MotifLocation feat.Feature
	MotifStart    int
	MotifEnd      int
	MotifScore    float64
	MotifProb     float64
	MotifSeq      seq.Sequence
	MotifOrient   feat.Orientation
	Moltype       feat.Moltype
}

func (*Feature) Description

func (f *Feature) Description() string

func (*Feature) End

func (f *Feature) End() int

func (*Feature) Len

func (f *Feature) Len() int

func (*Feature) Location

func (f *Feature) Location() feat.Feature

func (*Feature) MolType

func (f *Feature) MolType() feat.Moltype

func (*Feature) Name

func (f *Feature) Name() string

func (*Feature) Orientation

func (f *Feature) Orientation() feat.Orientation

func (*Feature) Start

func (f *Feature) Start() int

type PWM

type PWM struct {
	Format string // Format for probability values in attributes.
	// contains filtered or unexported fields
}

func New

func New(matrix [][]float64) (m *PWM)

func (*PWM) Search

func (m *PWM) Search(s Sequence, start, end int, minScore float64) []feat.Feature

type Sequence

type Sequence interface {
	seq.Sequence
	Moltype() feat.Moltype
	Orientation() feat.Orientation
}