decisionMatrix-class: decisionMatrix class

In Simon-Coetzee/footprintR: StatePaintR: a tool for creating and documenting reproducible chromatin state annotations from StateHub

Description

decisionMatrix class

Usage

## S4 method for signature 'decisionMatrix'
decisionMatrix(object)

## S4 method for signature 'decisionMatrix'
abstractionLayer(object)

## S4 method for signature 'decisionMatrix'
stateColors(object)

Arguments

object

decisionMatrix.

Value

an object of class decisionMatrix, normally made in response to a query to StateHub with get.decision.matrix

Methods (by generic)

• decisionMatrix: Extract Descision Matrix from descisionMatrix object

• abstractionLayer: Extract abstraction layer from descisionMatrix object

• stateColors: Extract color information from descisionMatrix object

Slots

id

character. a unique ID that refers to a model revision

name

character. The name of the model on StateHub

author

character. The author of the model on StateHub

revision

character. The revision of the model. A time stamp

description

character. A short description of the model.

abstraction.layer

list. A description of the relationship between the precise data type (e.g. a chromatin mark like H3K27ac) and feature describing the functional category in the decision.matrix (e.g. Regulatory).

decision.matrix

matrix. The description of what combination of features are required to call a state.

state.colors

character. The color to assign to each state.

Examples

load(system.file("extdata", "poised.promoter.model.rda", package = "StatePaintR"))
poised.promoter.model
decisionMatrix(poised.promoter.model)
abstractionLayer(poised.promoter.model)
stateColors(poised.promoter.model)

Simon-Coetzee/footprintR documentation built on May 9, 2019, 1:31 p.m.