Man pages for kevin-allen/relectro
Analysis of electrophysiological data

animalNameFromSessionNameGet animal name from session name
autocorrelationDoughnut-methodsCalculate the spatial autocorrelation of the firing rate maps...
autocorrelationDoughnutRotate-methodsGet the rotated region of the spatial autocorrelation of the...
autocorrelationNoFields-methodsCalculate the spatial autocorrelation of the firing rate maps...
bandPassFilterApply a band-pass filter to a signal
borderDetection-methodsDetect the border pixels in an environment and return a...
borderScore-methodsCalculate border scores from the firing maps
boxplotTwoFactorsPlot a boxplot with 2 factors
brainRegionFromCluNo-methodsGet the brain region from a list of cluNo
CellGroup-classAn S4 class representing a group of cells
centerOfMassCalculate the center of mass of a matrix, numeric or integer
checkIntegrityPositrackDataCheck the integrity of positrack data read from positrack...
checkIntegrityUpCheck the integrity of the up.
cluNoFromCluIdGet cluNo from cluId
clusterIsolationCheckCheck if clusters of a recording session are well isolated...
colorScalePlotPlot a color scale for the firing rate maps
containsElectrodeLocation-methodsCheck if the session had an electrode in a particular brain...
containsEnvironment-methodsCheck if the session had a trial in a given environment
containsStimulation-methodsCheck if the session had a trial in a given stimulation type
copyDatabase-methodsCreate a copy of the data from an experiment
copyRecSessionFiles-methodsMake a copy of the files of the recording session in another...
cor.diffPerform r-to-Z transform to get significance of difference...
createSpkFileCreate the spk file for each tetrode Use the traces and spike...
crossRefractoryRatio-methodsGet the cross refractory ratio of each cluster from its...
DatFiles-classA class representing one or more .dat files
datFilesGetChannels-methodsFunction to read from several channels from a group of dat...
datFilesGetOneChannel-methodsFunction to read one channel from a group of dat files
datFilesSamples-methodsGet the number of samples per file and file size
datFilesSet-methodsFunction to set the parameters of a DatFile object
deleteClusterDelete a specific cluster in a recording session
detectDownsDetect the negative deflection of a ttl pulse in a vector
detectFiringFields-methodsDetect firing fields in the firing rate maps of a...
detectSpikesFromTraceDetect spikes times in a filtered signal.
detectSpikesTetrodesDetect spikes on the channels of a tetrode.
detectUpsDetect the positive deflection of a ttl pulse in a vector
directionFilter-methodsSet position data to NA if animal's direction was not the one...
ElectroProject-classA S4 class to represent an electrophysiological project...
fileExists-methodsCheck if the session directory contains a file ending with...
firingRateHisto-methodsCalculate the firing rate histograms of neurons using a...
firingRateMap2d-methodsCalculate the firing rate maps of neurons using a SpikeTrain...
firingRateMapAutoPlotPlot a single spatial autocorrelation map
firingRateMapAutosPlotPlot a several spatial autocorrelation maps on the same page
firingRateMapCenterOfMass-methodsCalculate the center of mass of the firing rate maps in a...
firingRateMapCorrelation-methodsCalculate a Pearson correlation coefficients between the...
firingRateMapCorrelationRotation-methodsCalculate a Pearson correlation coefficients between maps of...
firingRateMapPlotPlot a single firing rate map
firingRateMapsPlotPlot several firing rate maps on the same page
firingRateMapsRotation-methodsRotate the firing rate maps of a SpatialProperties2d object
getClusteredSessionList-methodsReturn a list of clustered RecSession objects
getHistoStats-methodsCalculate spatial statistics of the firing rate histograms of...
getHistoStatsShuffle-methodsGet random values for statistics of the firing rate...
getIntervalsAtDirection-methodsGet time intervals at which the animal ran in a given...
getIntervalsAtHeadDirection-methodsGet time intervals at which the animal's head direction is in...
getIntervalsAtSpeed-methodsGet time intervals at which the speed of the animal was...
getIntervalsEnvironment-methodsGet the time intervals in sample values for trials in a given...
getIntervalsStimulation-methodsGet the time intervals in sample values for trials for a...
getIsClustered-methodsIs the recording session clustered?
getIsEarlyProcessed-methodsHas the spike extraction been run on the recording session?
getMapStats-methodsCalculate spatial statistics of the firing rate maps of...
getMapStatsShuffle-methodsCalculate random spatial statistics of the firing rate maps...
getRecSession-methodsReturn a RecSession object from the list in an ElectroProject...
getRecSessionObjects-methodsLoad a set of objects that are session specific
getSessionListFromSessionNames-methodsReturn a list of RecSession objects from a character vectors...
getSessionList-methodsReturn a list of RecSession objects that have some common...
getSpeedAtResValues-methodsGet the speed of the animal at given time points
getWaveformMatrixGet the waveform matrix, one spike per row
gridScore-methodsCalculate the grid scores from the spatial autocorrelations
gridSpacing-methodsCalculate the grid spacing from the spatial autocorrelations
hdHistoAsDataFrame-methodsReturn the hd histos as a data.frame
HeadDirection-classAn S4 class used to get head direction histograms and...
headDirectionHisto-methodsCalculate the head direction rate histograms of neurons using...
headDirectionPolarPlotPolar plot of firing rate as a function of head direction
headDirectionPolarPlotsPlot several polar plot with firing rate as a function of...
headDirectionStats-methodsCalculate the head direction statistics for the head...
headDirectionStatsShuffle-methodsCalculate the random head direction statistics for the head...
histoStatsAsDataFrame-methodsReturn the histo stats as data.frame.
identifySpikeTimesDetect spike times using filtered signal and root mean square...
ifrAssociation-methodsCalculate the correlation coefficient between the...
ifr-methodsCalculate the instantaneous firing rate from the spike...
isolationDistance-methodsGet the isolation distance of each cluster
joinIntervalsANDJoin two sets of intervals using an AND logic
linearizeLinearTrack-methodsLinearize the position data
linearRatePlotPlot a linear rate histogram from a SpatialProperties1D...
linearRatePlotsPlot several linear rate histograms from a...
loadCellGroup-methodsLoad the information regarding a group of cells
loadPositrack-methodsLoad position data from the .whl and .whd files
loadRecSession-methodsLoad the data regarding a recording session
loadSessionsInList-methodsCreate a List of RecSessions objects from the SessionNameList
loadSpikeTrain-methodsLoad the spike train from the .clu and .res files
makePairsReturns possible pairs from one or two vectors of values
mapsAsDataFrame-methodsReturn the firing rate maps in a data.frame
mapSpatialAutocorrelation-methodsCalculate the spatial autocorrelation of the firing rate maps...
meanFiringRate-methodsCalculate the mean firing rate (Hz) of each neuron in a...
meanWaveform-methodsCalculate the mean waveform of neurons in a recording...
mergeSimultaneousSpikesMerge simulatenous spikes that were detected on different...
mergeTetrodeSpecificResCluFilesMerge tetrode specific clu and res file into a main res and...
modeRelectroGet the mode of a distribution
pathPlotPlot the animal path
percentileFiringRateMaps-methodsGet a given percentile from the firing rate maps of a...
plotPointsPlot points in 2d
plotSimulatedRawTracePlot the raw traces simulation generated by the...
plotSpikeDetectionSegmentPlot the raw traces of a tetrode together with spike times of...
Positrack-classAn S4 class representing the path of an animal during a...
powerRootMeanSquareCalculate the root mean square within a sliding window
rateHistoAsDataFrame-methodsReturn the firing rate histograms as a data.frame.
readFetFileRead a fet file
recordingDate-methodsGet the recording date of a recSession, taken from session...
RecSession-classA S4 class to represent a recording session.
refractoryRatio-methodsGet refractory ratio of each cluster from its spike-time...
runOnSessionList-methodsRunning a function on a set of recording sessions
semGet the standard error of the mean
sessionNameFromCluIdGet session name from cluId
sessionNamesFromSessionListGet a character vector with the session names of a list of...
setCellList-methodsSet the list of cells to limit the analysis to these cells
setEvents-methodsSet some events for spike-time crosscorrelation to the...
setIntervals-methodsSet time intervals to limit the period used in the analysis
setInvalidOutsideInterval-methodsSet position data outside time intervals to NA
setPositrack-methodsset position values from arguments
setSessionList-methodsCreate a list of RecSession objects for the ElectroProject
setSpikeTrain-methodsSet new spike trains
shiftShift values in a vector by a certain number of places and in...
shiftHdRandom-methodsShift the head direction data of the animal of a random...
shiftLinRandom-methodsShift the linear position data of the animal of a random...
shiftPositionRandom-methodsShift the position of the animal of a random amount larger...
shiftPositionVectorShift a the values of a vector by a random amount that is at...
shiftPositionVectorsShift a the values of two vectors by a random amount that is...
shiftSpeedRandom-methodsShift the speed of the animal of a random amount larger than...
simulateRawTraceGenerate raw traces with some background gaussian noise and...
smoothGaussianSmooth the values in a numeric vector using a Gaussian kernel
smoothhd-methodsApply some smoothing to the hd array
smoothxy-methodsApply some smoothing to the x and y position data
sortRecSessionListChronologicallySort a list of RecSession objects according to the recording...
SpatialProperties1d-classA S4 class to analyze spatial properties in a 1D environment
SpatialProperties2d-classA S4 class to analyze spatial properties in 2D environments
speedFilter-methodsSet position data to NA for which the animal speed was not...
speedRateTuningCurve-methodsSpeed-rate tuning curve from spike train and positrack
speedScore-methodsSpeed scores from spike train and positrack
speedScoreShuffle-methodsRandom speed scores from spike train and positrack
spikeDetectionAccuracyAssess the quality of spike detection with simulated data.
spikeDistanceMetric-methodsGet the spike distance metric of the spikes
spikeExtractionSessionPerform the spike extraction for a recording session
spikeExtractionTetrodeTrialByTrialPerform the spike extraction for a given tetrode, reading...
spikeGeoFeatureOneSpikeGet the geometrical features of a single waveform
spikeGeoFeaturesGet the geometrical features of the spikes, treating each...
spikeOnPath-methodsReturn the data to plot spikes on the path of the animal
spikeOnPathPlotPlot a spikes on the animal path
spikePCADo PCA analysis on the spike waveforms, treating each channel...
spikeTimeAutocorrelationAsDataFrame-methodsGet spike-time autocorrelation as data.frame
spikeTimeAutocorrelationCenterOfMass-methodsCalculate spike-time autocorrelation center of mass
spikeTimeAutocorrelation-methodsCalculate the spike-time autocorrelation
spikeTimeAutocorrelationPlotPlot a single spike-time autocorrelation
spikeTimeAutocorrelationsPlotPlot several spike-time autocorrelation plot on the same page
spikeTimeCrosscorrelationAsDataFrame-methodsGet spike-time crosscorelation between cells as data.frame
spikeTimeCrosscorrelationEventsAsDataFrame-methodsGet spike-time crosscorelation to events as data.frame
spikeTimeCrosscorrelationEvents-methodsCalculate the spike-time crosscorrelation between the spike...
spikeTimeCrosscorrelation-methodsCalculate the spike-time crosscorrelation between the spike...
SpikeTrain-classA S4 class to represent the spike trains of one recording...
spikeTriggeredFiringRateMap2d-methodsCalculate the spike-triggered firing rate maps of neurons...
spikeTriggeredHeadDirectionCrossHisto-methodsCalculate the spike-triggered head-direction crosscorrelation...
spikeTriggeredHeadDirectionHisto-methodsCalculate the spike-triggered head-direction histogram using...
SpikeWaveform-classA S4 class to represent the spike waveforms of neurons
spikeWaveformFromTracesCreate the spike waveform array Returns a 3D array with the...
statsAsDataFrame-methodsReturn firing rate map statisitcs as a data.frame
timeWithinIntervalsGet a logical vector to know if time points are within a...
waveformCharacteristics-methodsCalculate waveform characteristics from the mean waveform of...
whdAlignedTtlPositrackTry to realign the up part of ttl pulses from .dat file and...
whdFromPositrackCreate whd files for each trial (or .dat file) and for the...
writeFetFileWrite the fet file The first line of the fet file contains a...
writeMmFileWrite the mm file for each tetrode
writeParTetrodeFileWrite the par file for each tetrode
kevin-allen/relectro documentation built on May 28, 2018, 4:12 p.m.