dot-Overview: PatchR - An environment for working with electrophysiology...

In moritzlindner/PatchR: An environment for working with ephys (PatchClamp) recordings

PatchR - An environment for working with electrophysiology recordings

Description

Core component of PatchR is the PRecording class, which stores a series imported from a Patchmaster .dat file or an Axon .abf file. Several checks are implemented into the PRecording class to assure data integrity is maintained.
Multiple recordings PRecording objects containing identically shaped data (i.e. recorded witht the same protocol) can be stored and processed within the PCollection class using mostly identical commands and syntax.
Import procedures are currently implemented for HEKA's PachtMaster .dat and Axon Instruments .abf file format.

File operations

• ImportPRecording (for PRecording objects)
  

• AddTrace (for PRecording objects)
  

• newPCollection (for PCollection objects)
  

• AddPRecording (for PCollection objects)
  

• AddPRecording (for PCollection objects)
  

• Load (for PRecording and PCollection objects)
  

• Save (for PRecording and PCollection objects)
  

Accession functions

• GetData
  

• GetPlot
  

• GetMetaData
  

• GetRecParam
  

• GetCSlow
  

• GetSweepNames
  

• GetTimeTrace
  

• GetTraceNames
  

• GetGroupMembers
  

• GetRecordingNames
  

• GetPlotNames
  

• GetPlot
  

• as.data.frame()
  

Measurement functions

• Measure
  

• MeasureStimResp
  

• MeasureSweeps
  

Visuaization functions

• BuildStimRespPlot
  

• BuildGroupComparisonPlot (for PCollection objects)
  

• BuildRecordingPlot (for PCollection objects)
  

• BuildRecordingPlot (for PRecording objects)
  

• Inspect (for PRecording and PCollection objects)
  

Math, conversion and subsampling functions

• CurrentDensity (for PRecording objects)
  

• GetData
  

• Calculate_IV - Outdated
  

• apply() for PRecording and lapply() for PCollection
  

Author(s)

Moritz Lindner

Examples

## Not run: 
# Example 1
# import a PatchMaster file
tmp<-ImportPRecording("test.dat",series = 1,traces = c(1,2))

# build a Plot superimposing all sweeps and inspect interactivley
tmp<-BuildRecordingPlot(tmp)
tmp<-InspectSeries(tmp, Trace = "I.mon")

# apply any function to the PRecording object, in this case, make mean over all sweeps
tmp<-apply(tmp, "Sweep", mean, ReturnPObject = TRUE)

# and return as data.frame
as.data.frame(tmp)

# Example 2

exp<-newPCollection(list(tmp,tmp),Names=c("A","B"),Group=c("Generic1","Generic2"))
AddMetaData(exp, #add as metadata to PCollection
            lapply(exp, # for each PRecording stored in PCollection
                   function(x){
                      apply( # average over time
                            getData(x,
                            # extract values from I-mon trace,
                            # Sweep 15, between 1 and 1.19 s only
                                    Traces="I-mon",
                                    Time =c(1,1.19),
                                    Sweeps=getSweepNames(x)[c(15)]),
                            "Time",
                            mean)
                   }
            )
)

exp@MetaData


## End(Not run)

moritzlindner/PatchR documentation built on April 30, 2024, 1:40 a.m.