CollectSpikesFromSweeps: Read in Igor Pro exported text file of Nclamp spike times

In jefferis/gphys: Analyse Electrophysiology Data Acquired by 'Neuromatic' / 'Igor Pro'

Description

The list of spiketimes has two columns, Time and Wave, where wave is the number of the wave within each sweepfile containing the spike. xlim and stimRange are kept as attributes that will be used for plots * fixChannels expects a named vector of any channels that need to have different odour names. This can be used to fix an error in the original ODD config file. * If spike time txt files have been placed in a subdirectory, then that subdirectory must be specified using the subdir argument. * However it is expected that the corresponding pxp and odd config files remain in the top level directory for the cell.

Usage

CollectSpikesFromSweeps(sweepdir, sweeps, subdir = "", xlim, stimRange,
  fixChannels = NULL, subset = NULL)

Arguments

sweepdir	directory containing Nclamp pxp sweep files
sweeps	Vector of sweeps to include (e.g. 1:7) or character regex which sweeps must match.
subdir	subdirectory containing group of spike times txt files
xlim	time range of sweeps
stimRange	time range of stimulus
fixChannels	Optional named integer vector that remaps some bad numeric channels to correct odours. FIXME shouldn't we fix channels as well.
subset	Numeric vector of channels or character vector of odours

Value

list (with class spiketimes) containing times for each sweep

Author(s)

jefferis

Examples

## Not run: 
# Collect from absolute path (what you will probably typically do)
spikes=CollectSpikesFromSweeps(
  '/Volumes/JData/JPeople/Jonny/physiology/data/nm20120514c2',subdir='BLOCK B')

## End(Not run)
# If you have your data in a single folder hierarchy, you can that as the
# data directory.
# Here we set the data directory to folder containing gphys example data
options(gphys.datadir=system.file('igor','spikes',package='gphys'))
spikes=CollectSpikesFromSweeps('nm20120514c2',subdir='BLOCKB')
# Finally an example specifying the exact sweeps to load
spikes=CollectSpikesFromSweeps("nm20110811c0",c(0,1,3))
# and plotting them
plot(spikes,xlim=c(2000,4000),odourRange=c(2000,3000))

jefferis/gphys documentation built on June 5, 2019, 9:45 p.m.