Man pages for kevin-allen/relectro
Analysis of electrophysiological data
| animalNameFromSessionName | Get animal name from session name |
| autocorrelationDoughnut-methods | Calculate the spatial autocorrelation of the firing rate maps... |
| autocorrelationDoughnutRotate-methods | Get the rotated region of the spatial autocorrelation of the... |
| autocorrelationNoFields-methods | Calculate the spatial autocorrelation of the firing rate maps... |
| bandPassFilter | Apply a band-pass filter to a signal |
| borderDetection-methods | Detect the border pixels in an environment and return a... |
| borderScore-methods | Calculate border scores from the firing maps |
| boxplotTwoFactors | Plot a boxplot with 2 factors |
| brainRegionFromCluNo-methods | Get the brain region from a list of cluNo |
| CellGroup-class | An S4 class representing a group of cells |
| centerOfMass | Calculate the center of mass of a matrix, numeric or integer |
| checkIntegrityPositrackData | Check the integrity of positrack data read from positrack... |
| checkIntegrityUp | Check the integrity of the up. |
| cluNoFromCluId | Get cluNo from cluId |
| clusterIsolationCheck | Check if clusters of a recording session are well isolated... |
| colorScalePlot | Plot a color scale for the firing rate maps |
| containsElectrodeLocation-methods | Check if the session had an electrode in a particular brain... |
| containsEnvironment-methods | Check if the session had a trial in a given environment |
| containsStimulation-methods | Check if the session had a trial in a given stimulation type |
| copyDatabase-methods | Create a copy of the data from an experiment |
| copyRecSessionFiles-methods | Make a copy of the files of the recording session in another... |
| cor.diff | Perform r-to-Z transform to get significance of difference... |
| createSpkFile | Create the spk file for each tetrode Use the traces and spike... |
| crossRefractoryRatio-methods | Get the cross refractory ratio of each cluster from its... |
| DatFiles-class | A class representing one or more .dat files |
| datFilesGetChannels-methods | Function to read from several channels from a group of dat... |
| datFilesGetOneChannel-methods | Function to read one channel from a group of dat files |
| datFilesSamples-methods | Get the number of samples per file and file size |
| datFilesSet-methods | Function to set the parameters of a DatFile object |
| deleteCluster | Delete a specific cluster in a recording session |
| detectDowns | Detect the negative deflection of a ttl pulse in a vector |
| detectFiringFields-methods | Detect firing fields in the firing rate maps of a... |
| detectSpikesFromTrace | Detect spikes times in a filtered signal. |
| detectSpikesTetrodes | Detect spikes on the channels of a tetrode. |
| detectUps | Detect the positive deflection of a ttl pulse in a vector |
| directionFilter-methods | Set position data to NA if animal's direction was not the one... |
| ElectroProject-class | A S4 class to represent an electrophysiological project... |
| fileExists-methods | Check if the session directory contains a file ending with... |
| firingRateHisto-methods | Calculate the firing rate histograms of neurons using a... |
| firingRateMap2d-methods | Calculate the firing rate maps of neurons using a SpikeTrain... |
| firingRateMapAutoPlot | Plot a single spatial autocorrelation map |
| firingRateMapAutosPlot | Plot a several spatial autocorrelation maps on the same page |
| firingRateMapCenterOfMass-methods | Calculate the center of mass of the firing rate maps in a... |
| firingRateMapCorrelation-methods | Calculate a Pearson correlation coefficients between the... |
| firingRateMapCorrelationRotation-methods | Calculate a Pearson correlation coefficients between maps of... |
| firingRateMapPlot | Plot a single firing rate map |
| firingRateMapsPlot | Plot several firing rate maps on the same page |
| firingRateMapsRotation-methods | Rotate the firing rate maps of a SpatialProperties2d object |
| getClusteredSessionList-methods | Return a list of clustered RecSession objects |
| getHistoStats-methods | Calculate spatial statistics of the firing rate histograms of... |
| getHistoStatsShuffle-methods | Get random values for statistics of the firing rate... |
| getIntervalsAtDirection-methods | Get time intervals at which the animal ran in a given... |
| getIntervalsAtHeadDirection-methods | Get time intervals at which the animal's head direction is in... |
| getIntervalsAtSpeed-methods | Get time intervals at which the speed of the animal was... |
| getIntervalsEnvironment-methods | Get the time intervals in sample values for trials in a given... |
| getIntervalsStimulation-methods | Get the time intervals in sample values for trials for a... |
| getIsClustered-methods | Is the recording session clustered? |
| getIsEarlyProcessed-methods | Has the spike extraction been run on the recording session? |
| getMapStats-methods | Calculate spatial statistics of the firing rate maps of... |
| getMapStatsShuffle-methods | Calculate random spatial statistics of the firing rate maps... |
| getRecSession-methods | Return a RecSession object from the list in an ElectroProject... |
| getRecSessionObjects-methods | Load a set of objects that are session specific |
| getSessionListFromSessionNames-methods | Return a list of RecSession objects from a character vectors... |
| getSessionList-methods | Return a list of RecSession objects that have some common... |
| getSpeedAtResValues-methods | Get the speed of the animal at given time points |
| getWaveformMatrix | Get the waveform matrix, one spike per row |
| gridScore-methods | Calculate the grid scores from the spatial autocorrelations |
| gridSpacing-methods | Calculate the grid spacing from the spatial autocorrelations |
| hdHistoAsDataFrame-methods | Return the hd histos as a data.frame |
| HeadDirection-class | An S4 class used to get head direction histograms and... |
| headDirectionHisto-methods | Calculate the head direction rate histograms of neurons using... |
| headDirectionPolarPlot | Polar plot of firing rate as a function of head direction |
| headDirectionPolarPlots | Plot several polar plot with firing rate as a function of... |
| headDirectionStats-methods | Calculate the head direction statistics for the head... |
| headDirectionStatsShuffle-methods | Calculate the random head direction statistics for the head... |
| histoStatsAsDataFrame-methods | Return the histo stats as data.frame. |
| identifySpikeTimes | Detect spike times using filtered signal and root mean square... |
| ifrAssociation-methods | Calculate the correlation coefficient between the... |
| ifr-methods | Calculate the instantaneous firing rate from the spike... |
| isolationDistance-methods | Get the isolation distance of each cluster |
| joinIntervalsAND | Join two sets of intervals using an AND logic |
| linearizeLinearTrack-methods | Linearize the position data |
| linearRatePlot | Plot a linear rate histogram from a SpatialProperties1D... |
| linearRatePlots | Plot several linear rate histograms from a... |
| loadCellGroup-methods | Load the information regarding a group of cells |
| loadPositrack-methods | Load position data from the .whl and .whd files |
| loadRecSession-methods | Load the data regarding a recording session |
| loadSessionsInList-methods | Create a List of RecSessions objects from the SessionNameList |
| loadSpikeTrain-methods | Load the spike train from the .clu and .res files |
| makePairs | Returns possible pairs from one or two vectors of values |
| mapsAsDataFrame-methods | Return the firing rate maps in a data.frame |
| mapSpatialAutocorrelation-methods | Calculate the spatial autocorrelation of the firing rate maps... |
| meanFiringRate-methods | Calculate the mean firing rate (Hz) of each neuron in a... |
| meanWaveform-methods | Calculate the mean waveform of neurons in a recording... |
| mergeSimultaneousSpikes | Merge simulatenous spikes that were detected on different... |
| mergeTetrodeSpecificResCluFiles | Merge tetrode specific clu and res file into a main res and... |
| modeRelectro | Get the mode of a distribution |
| pathPlot | Plot the animal path |
| percentileFiringRateMaps-methods | Get a given percentile from the firing rate maps of a... |
| plotPoints | Plot points in 2d |
| plotSimulatedRawTrace | Plot the raw traces simulation generated by the... |
| plotSpikeDetectionSegment | Plot the raw traces of a tetrode together with spike times of... |
| Positrack-class | An S4 class representing the path of an animal during a... |
| powerRootMeanSquare | Calculate the root mean square within a sliding window |
| rateHistoAsDataFrame-methods | Return the firing rate histograms as a data.frame. |
| readFetFile | Read a fet file |
| recordingDate-methods | Get the recording date of a recSession, taken from session... |
| RecSession-class | A S4 class to represent a recording session. |
| refractoryRatio-methods | Get refractory ratio of each cluster from its spike-time... |
| runOnSessionList-methods | Running a function on a set of recording sessions |
| sem | Get the standard error of the mean |
| sessionNameFromCluId | Get session name from cluId |
| sessionNamesFromSessionList | Get a character vector with the session names of a list of... |
| setCellList-methods | Set the list of cells to limit the analysis to these cells |
| setEvents-methods | Set some events for spike-time crosscorrelation to the... |
| setIntervals-methods | Set time intervals to limit the period used in the analysis |
| setInvalidOutsideInterval-methods | Set position data outside time intervals to NA |
| setPositrack-methods | set position values from arguments |
| setSessionList-methods | Create a list of RecSession objects for the ElectroProject |
| setSpikeTrain-methods | Set new spike trains |
| shift | Shift values in a vector by a certain number of places and in... |
| shiftHdRandom-methods | Shift the head direction data of the animal of a random... |
| shiftLinRandom-methods | Shift the linear position data of the animal of a random... |
| shiftPositionRandom-methods | Shift the position of the animal of a random amount larger... |
| shiftPositionVector | Shift a the values of a vector by a random amount that is at... |
| shiftPositionVectors | Shift a the values of two vectors by a random amount that is... |
| shiftSpeedRandom-methods | Shift the speed of the animal of a random amount larger than... |
| simulateRawTrace | Generate raw traces with some background gaussian noise and... |
| smoothGaussian | Smooth the values in a numeric vector using a Gaussian kernel |
| smoothhd-methods | Apply some smoothing to the hd array |
| smoothxy-methods | Apply some smoothing to the x and y position data |
| sortRecSessionListChronologically | Sort a list of RecSession objects according to the recording... |
| SpatialProperties1d-class | A S4 class to analyze spatial properties in a 1D environment |
| SpatialProperties2d-class | A S4 class to analyze spatial properties in 2D environments |
| speedFilter-methods | Set position data to NA for which the animal speed was not... |
| speedRateTuningCurve-methods | Speed-rate tuning curve from spike train and positrack |
| speedScore-methods | Speed scores from spike train and positrack |
| speedScoreShuffle-methods | Random speed scores from spike train and positrack |
| spikeDetectionAccuracy | Assess the quality of spike detection with simulated data. |
| spikeDistanceMetric-methods | Get the spike distance metric of the spikes |
| spikeExtractionSession | Perform the spike extraction for a recording session |
| spikeExtractionTetrodeTrialByTrial | Perform the spike extraction for a given tetrode, reading... |
| spikeGeoFeatureOneSpike | Get the geometrical features of a single waveform |
| spikeGeoFeatures | Get the geometrical features of the spikes, treating each... |
| spikeOnPath-methods | Return the data to plot spikes on the path of the animal |
| spikeOnPathPlot | Plot a spikes on the animal path |
| spikePCA | Do PCA analysis on the spike waveforms, treating each channel... |
| spikeTimeAutocorrelationAsDataFrame-methods | Get spike-time autocorrelation as data.frame |
| spikeTimeAutocorrelationCenterOfMass-methods | Calculate spike-time autocorrelation center of mass |
| spikeTimeAutocorrelation-methods | Calculate the spike-time autocorrelation |
| spikeTimeAutocorrelationPlot | Plot a single spike-time autocorrelation |
| spikeTimeAutocorrelationsPlot | Plot several spike-time autocorrelation plot on the same page |
| spikeTimeCrosscorrelationAsDataFrame-methods | Get spike-time crosscorelation between cells as data.frame |
| spikeTimeCrosscorrelationEventsAsDataFrame-methods | Get spike-time crosscorelation to events as data.frame |
| spikeTimeCrosscorrelationEvents-methods | Calculate the spike-time crosscorrelation between the spike... |
| spikeTimeCrosscorrelation-methods | Calculate the spike-time crosscorrelation between the spike... |
| SpikeTrain-class | A S4 class to represent the spike trains of one recording... |
| spikeTriggeredFiringRateMap2d-methods | Calculate the spike-triggered firing rate maps of neurons... |
| spikeTriggeredHeadDirectionCrossHisto-methods | Calculate the spike-triggered head-direction crosscorrelation... |
| spikeTriggeredHeadDirectionHisto-methods | Calculate the spike-triggered head-direction histogram using... |
| SpikeWaveform-class | A S4 class to represent the spike waveforms of neurons |
| spikeWaveformFromTraces | Create the spike waveform array Returns a 3D array with the... |
| statsAsDataFrame-methods | Return firing rate map statisitcs as a data.frame |
| timeWithinIntervals | Get a logical vector to know if time points are within a... |
| waveformCharacteristics-methods | Calculate waveform characteristics from the mean waveform of... |
| whdAlignedTtlPositrack | Try to realign the up part of ttl pulses from .dat file and... |
| whdFromPositrack | Create whd files for each trial (or .dat file) and for the... |
| writeFetFile | Write the fet file The first line of the fet file contains a... |
| writeMmFile | Write the mm file for each tetrode |
| writeParTetrodeFile | Write the par file for each tetrode |
