R: summary methods for the MACPET classes.

summary {MACPET}

R Documentation

summary methods for the MACPET classes.

Description

Different summary methods for the classes in the MACPET package.

Usage

## S3 method for class 'PSelf'
summary(object, ...)

## S4 method for signature 'PSelf'
summary(object, ...)

## S3 method for class 'PSFit'
summary(object, threshold = NULL, ...)

## S4 method for signature 'PSFit'
summary(object, threshold = NULL, ...)

## S3 method for class 'PIntra'
summary(object, heatmap = FALSE, ...)

## S4 method for signature 'PIntra'
summary(object, heatmap = FALSE, ...)

## S3 method for class 'PInter'
summary(object, heatmap = FALSE, ...)

## S4 method for signature 'PInter'
summary(object, heatmap = FALSE, ...)

## S3 method for class 'GenomeMap'
summary(object, threshold = NULL, ...)

## S4 method for signature 'GenomeMap'
summary(object, threshold = NULL, ...)

Arguments

`object`	An object of correct class used to create different summaries.
`...`	Further arguments to be passed to the summary function.
`threshold`	A numeric representing the FDR cut-off or summarizing singificant peaks (or interactions), if NULL the summary is based on all the peaks found.
`heatmap`	TRUE or FALSE indicating whether the user wants to plot a heat-map plot for the Intra/Inter-chromosomal PET counts within chromosomes or between different chromosomes.

Value

A summary of the object and a heat-map plot depending on the class of the input.

Author(s)

Ioannis Vardaxis, ioannis.vardaxis@ntnu.no

References

Vardaxis I, Drabløs F, Rye M and Lindqvist BH (2018). MACPET: Model-based Analysis for ChIA-PET. To be published.

Examples


#load Self-ligated data: (class=PSelf)
load(system.file('extdata', 'MACPET_pselfData.rda', package = 'MACPET'))
class(MACPET_pselfData)
summary(MACPET_pselfData)

#load Self-ligated data: (class=PSFit)
load(system.file('extdata', 'MACPET_psfitData.rda', package = 'MACPET'))
class(MACPET_psfitData)
summary(MACPET_psfitData)
summary(MACPET_psfitData,threshold=1e-5)

#load Intra-chromosomal data: (class=PIntra)
load(system.file('extdata', 'MACPET_pintraData.rda', package = 'MACPET'))
class(MACPET_pintraData)
summary(MACPET_pintraData)
requireNamespace('ggplot2')
requireNamespace('reshape2')
summary(MACPET_pintraData,heatmap=TRUE)#sample data, not good heatmap plot.

#load Inter-chromosomal data: (class=PInter)
load(system.file('extdata', 'MACPET_pinterData.rda', package = 'MACPET'))
class(MACPET_pinterData)
summary(MACPET_pinterData)
requireNamespace('ggplot2')
requireNamespace('reshape2')
summary(MACPET_pinterData,heatmap=TRUE)#sample data, not good heatmap plot.

#load Interaction data: (class=GenomeMap)
load(system.file('extdata', 'MACPET_GenomeMapData.rda', package = 'MACPET'))
class(MACPET_GenomeMapData)
summary(MACPET_GenomeMapData)

[Package MACPET version 1.6.0 Index]