AnalysisStatistics {MACPET} | R Documentation |
AnalysisStatistics
prints and saves count statistics
for the current inputs of the peak-calling analysis.
AnalysisStatistics(x.self, x.intra = NULL, x.inter = NULL, file.out = NULL, threshold = 1e-05, savedir = NULL)
x.self |
|
x.intra |
An object of class |
x.inter |
An object of class |
file.out |
A string with the name of the output to be saved to
|
threshold |
A numeric indicating the FDR cut-off, used when
|
savedir |
A string with the directory to save the ouput file. If
|
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
.
Ioannis Vardaxis, ioannis.vardaxis@ntnu.no
Vardaxis I, Drabløs F, Rye M and Lindqvist BH (2018). MACPET: Model-based Analysis for ChIA-PET. To be published.
#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)