sanger.read.spikes: Read in a nexTimestamps file from Neuroexplorer and create a...
In sjemea: Multi electrode analysis

Description Usage Arguments Details Value Author(s) See Also Examples

The Genes to Cognition Project (G2C) uses Neuroexplorer to output spike times from an MEA recording. This function reads those text files and creates a "spikes" data structure.

1 2	sanger.read.spikes(filename, ids=NULL, time.interval=1, beg=NULL, end=NULL, min.rate=0)

`filename`	Name of the text file to be read in.
`ids`	Which electrodes should be kept.
`time.interval`	How often to estimate the firing rate.
`beg`	Start time of the recording.
`end`	End time of the recording.
`min.rate`	Minimum firing rate of an electrode.

This format is fairly simple; each column represents one channel, with the spikes recorded in that channel filling up the column. Since different channels are likely to record different numbers of spikes, empty values (just a TAB to next value) are found at the bottom of each spike train.

Text files can be compressed, using gzip, to save space. (The extension .gz is added to compresed files.) This compression aspect should be transparent to the end user – if a file is compresed, the filename can be given with or without the .gz extension. gzip is available for Windows (from http://www.gzip.org); "gzip *.nexTimestamps" will compress all timestamps, and "gzip -d *.nexTimestamps" will uncompress them.

Return the data structure 's'.

Stephen Eglen

jay.read.spikes compute.ns

data.file <- system.file("examples", "TC89_DIV15_A.nexTimestamps",
                         package = "sjemea")
s <- sanger.read.spikes( data.file, beg=400, end=700)
fourplot(s)