meaRtools: write_plate_summary_for_bursts – R documentation

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write_plate_summary_for_bursts

Prints bursting features

Description

The function reads the MEA data structure and uses the 'allb' list built using mi_find_bursts. It then prints all bursting features summary per well and per channel in _bursts.csv and _well_bursts.csv

Usage

write_plate_summary_for_bursts(s, outputdir)

Arguments

`s`	MEA data structure
`outputdir`	Output directory

Value

Output file _bursts.csv holds all features generated for bursts per well and per channel:

`treatment`	the treatment/genotype based on the experimental log file plan
`well`	well number
`nae`	number of active electrodes
`nAB`	number of electrodes with bursts
`duration`	total duration of bursts
`mean_dur`	mean duration of bursts
`mean_freq`	firing rate (Hz)
`nbursts`	number of bursts
`bursts_per_sec`	bursts/second.matrix(nrow=0,ncol=1)
`bursts_per_min`	bursts/min
`sd_dur`	sd of burst duration
`mean_freq_in_burst`	average frequency of spikes in a burst
`sd_freq_in_burst`	sd of frequency of spikes in a burst
`mean_spikes_in_burst`	mean number of spikes in a burst
`sd_spikes_in_burst`	sd of number of spikes in a burst
`total_spikes_in_burst`	total number of spikes in a bursts
`per_spikes_in_burst`	percent of spikes in a burst
`mean_isis`	mean ISI within a burst
`sd_isis`	sd ISI within a burst
`mean_ibis`	mean IBI
`sd_ibis`	sd of ibis
`cv_ibis`	Coefficient of variation of IBI (= mean_ibi/sd_ibi)
`file`	input recording file

Examples

data("S")  
output_dir = file.path(tempdir(),"Analysis")
print(paste0("Creating output folders under ",output_dir))
dir.create(output_dir)

s<-list(); s[[1]]<-S
write_plate_summary_for_bursts(s, output_dir)

meaRtools

Micro-Electro Array (MEA) Analysis

v1.0.4

GPL (>= 3)

Authors

Quanli Wang [aut, ctb], Sahar Gelfman [aut, ctb, cre], Diana Hall [aut, ctb], Ryan Dhindsa [aut, ctb], Matt Halvorsen [aut, ctb], Ellese Cotterill [aut, ctb], Tom Edinburgh [aut, ctb], Stephen J. Eglen [aut, ctb, ths]

Initial release

2018-7-1