litke.read.spikes: Read in the .mat file containing MEA data from Alan Litke

Description Usage Arguments Value METHOD References See Also Examples

View source: R/litke.R

Description

Read in the matlab file and process as a regular MEA.

Usage

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litke.read.spikes(filename, ids, time.interval, beg, end, corr.method)
iit.read.spikes(filename, ids, time.interval, beg, end)

Arguments

filename

Name of the text file to be read in.

ids

Optional vector of cell numbers that can be analysed, rather than analysing all electrodes in the recording. Warning: Not implemented in all readers.

time.interval

Bin width (in seconds) for estimating firing rate. Defaults to 1 second.

beg

Optional start time.

end

Optional end time.

corr.method

Which correlation method to use? Only 'ci' supported for the Likte reader.

Value

Return the data structure 's'.

METHOD

The data provided by Alan Litke is stored as a matlab file. There should be only one item in the file, which is the matrix containing the spikes.

The matrix contains one row per electrode. The first item in the row is the cell number; the second item is the electrode that recorded the cell. The remaining numbers are the spike times (which must be divided by 20000 to get time in seconds). All spike trains are zero-padded to be the same length.

As the matlab format is used, the R.matlab and Rcompression packages are required. These can be installed from R using:

install.packages(c('R.utils', 'R.matlab')) install.packages('Rcompression', repos = "http://www.omegahat.org/R")

(The IIT data also use a matlab format, and so the above installations are also needed for IIT.)

The location of each electrode is given in the data file ‘litke1layout’, see examples below.

References

This reader used for the Stafford et al. (2009) data in Neuron.

See Also

jay.read.spikes

Examples

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## Show the layout of the array.
show.litke.layout()

## The location of the file storing the electrode positions
system.file('data', 'litke1layout.txt', package='sjemea')

sjemea documentation built on May 21, 2017, 1:33 a.m.

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