AnalysisStatistics: Count Statistics for ChIA-PET.

In IoannisVardaxis/MACPET: Model based analysis for paired-end data

Description

AnalysisStatistics prints and saves count statistics for the current inputs of the peak-calling analysis.

Usage

AnalysisStatistics(x.self, x.intra = NULL, x.inter = NULL,
  file.out = NULL, threshold = 1e-05, savedir = NULL)

Arguments

x.self	An object of class PSelf or PSFit.
x.intra	An object of class PIntra (optional).
x.inter	An object of class PInter (optional).
file.out	A string with the name of the output to be saved to savedir. If NULL the function will only print the output.
threshold	A numeric indicating the FDR cut-off, used when class(x.self)=PSFit. If NULL, no threshold is applied.
savedir	A string with the directory to save the ouput file. If NULL then the function will only print the output.

Value

Based on the inputs, AnalysisStatistics prints the total Self-ligated, Intra- and Inter-chromosomal PETs, as well as the total regions, total candidate peaks and total significant peaks (if threshold!=NULL and class(x.self)=PSFit). If file.out and savedir are not NULL then it also saves the output to a csv file in savedir.

Author(s)

Ioannis Vardaxis, [e-mail]

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,PIntra, PInter

Examples

#Create a temporary test forder, or anywhere you want:
savedir=file.path(tempdir(),'MACPETtest')
dir.create(savedir)#where you will save the results

#load Inter-chromosomal data:
load(system.file('extdata', 'MACPET_pinterData.rda', package = 'MACPET'))
class(MACPET_pinterData)

#load Intra-chromosomal data:
load(system.file('extdata', 'MACPET_pintraData.rda', package = 'MACPET'))
class(MACPET_pintraData)

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

#Print analysis:
AnalysisStatistics(x.self=MACPET_pselfData,
                   x.intra=MACPET_pintraData,
                   x.inter=MACPET_pinterData,
                   file.out='AnalysisStats',
                   savedir=savedir)

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

#Print analysis:
AnalysisStatistics(x.self=MACPET_psfitData,
                   x.intra=MACPET_pintraData,
                   x.inter=MACPET_pinterData,
                   file.out='AnalysisStats',
                   savedir=savedir,
                   threshold=1e-5)

#-----delete test directory:
unlink(savedir,recursive=TRUE)

IoannisVardaxis/MACPET documentation built on Aug. 9, 2019, 12:11 p.m.