ConvertToPSelf: Convert GInteraction object to PSelf object

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

Description

ConvertToPSelf converts a GInteractions object to class to PSelf object.

Usage

ConvertToPSelf(object, ...)

## Default S3 method:
ConvertToPSelf(object, ...)

## S3 method for class 'GInteractions'
ConvertToPSelf(object, S2_BlackList, SA_prefix,
  S2_AnalysisDir, ...)

## S4 method for signature 'GInteractions'
ConvertToPSelf(object, S2_BlackList, SA_prefix,
  S2_AnalysisDir, ...)

Arguments

object	An object of GInteractions class.
...	not used.
S2_BlackList	See MACPETUlt.
SA_prefix	See MACPETUlt.
S2_AnalysisDir	The directory in which the object will be saved.

Details

MACPETUlt at State 2 separates the Inter-chromosomal, Intra-chromosomal and Self-ligated PETs by taking the paired-end BAM/SAM file as input. However the user might only have Self-ligated data available and already separated from the Inter/Intra-chromosomal PETs. ConvertToPSelf can then be used in the Self-ligated data to convert a GInteractions object containing only the Self-ligated PETs to a PSelf class for further analysis in Stage 3. The object will be saved in the S2_AnalysisDir directory with the name SA_prefix_pselfData. Note that if S2_BlackList==TRUE then the GInteractions object given as input has to include the genome name in the seqinfo slot. Also, the sequences lengths are mandatory in the seqinfo slot since they are used in stage 3 of the analysis.

Value

An object of class PSelf.

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

Examples

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

object=MACPET_pselfData
#--remove information and convert to GInteractions:
S4Vectors::metadata(object)=list(NULL)
class(object)='GInteractions'
#----input parameters
S2_BlackList=TRUE
SA_prefix='MACPET'
S2_AnalysisDir=file.path(tempdir(),'MACPETtest')
if(!dir.exists(S2_AnalysisDir)) dir.create(S2_AnalysisDir)

ConvertToPSelf(object=object,
                      S2_BlackList=S2_BlackList,
                      SA_prefix=SA_prefix,
                      S2_AnalysisDir=S2_AnalysisDir)
#load object:
rm(MACPET_pselfData)#old object
load(file.path(S2_AnalysisDir,'MACPET_pselfData'))
class(MACPET_pselfData)
#-----delete test directory:
unlink(S2_AnalysisDir,recursive=TRUE)

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