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, ...)

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

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

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

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 cutoff for summarizing singificant peaks, 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.

See Also

PSelf, PSFit, PInter,PIntra

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.

[Package MACPET version 1.0.0 Index]