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.

### See Also

`PSelf`, `PSFit`, `PInter`,`PIntra`, `GenomeMap`

### 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 1.12.0 Index]