ConvertToPSelf {MACPET} | R Documentation |
ConvertToPSelf
converts a GInteractions
object to
class to PSelf
object.
ConvertToPSelf(object, ...) ## Default S3 method: ConvertToPSelf(object, ...) ## S3 method for class 'GInteractions' ConvertToPSelf(object, S2_BlackList, SA_prefix, S2_AnalysisDir, ...)
object |
An object of |
... |
not used. |
S2_BlackList |
See |
SA_prefix |
See |
S2_AnalysisDir |
The directory in which the object will be saved. |
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.
An object of class PSelf
.
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.
#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)