htbGetRas: Creator for htbRas object

In keimochizuki/htb: Read and Analyze Neural Activities Acquired by TEMPO System

Creator for htbRas object

Description

Creates htbRas object from htbDb objects.

Usage

htbGetRas(
  db_data,
  db_event,
  alignment,
  incld = NULL,
  excld = NULL,
  cond = all,
  ch = NULL,
  event = NULL,
  title = NULL
)

Arguments

db_data	An htbDb object of spike or analog type that contains the data you want to align.
db_event	An htbDb object of event type used to align the data.
alignment	A named list. Each element of the list must be a vector of length two, that designate the range of the extracted data around the time of aligning event in standard xlim style in R, i.e., c(from, to). The name of the list is used as the name of the events to look at for the alignment.
incld	A named list. The task event(s) needed to exist within an arbitrary range from the aligning event (designated by alignment argument). Format is the same to that of alignment, i.e., all the elements must be vectors of length two indicating from and to of the temporal range, and the name of the list corresponds to the events to be checked. This argument can be a list of such named lists, in which case they are used separately used for each element of alignment.
excld	A named list. Same to incld but for task event(s) that must not exist within the range from aligning event.
cond	A function. Conditional function (either all() or any()) used in in/exclusion process. When all() is used, a period of data is accepted and incorporated into resulting htbRas object if all the in/exclusion criteria designated by incld and excld are fulfilled. When any() is used, a period of data is appended if any one or more criteria of incld and excld are fulfilled.
ch	Integer(s). The channel(s) of db_data to extract. When multiple channels are designated, htbGetRas() returns a list of htbRas objects (instead of an htbRas object) as a result of data extraction for each channel of the htbDb object with the same extraction settings.
event	Strings. The names of task events you want to include in returning htbRas object. The timing information of these events can be then used in further visualization and analysis (e.g., plotting the event when you draw a rastergram).
title	Strings. The titles for the extraction whose length equals to that of alignment.

Details

In order to assess the function of recorded neural activity, you need to examine the relationship between neuron's firing and other experimental factors such as task events. For example, some neurons may be activated at the time of visual cue presentation, while others may fire when the response is made. For this analysis, your first step will be aligning the neural activity by the occurrence of a given task event. In other words, you need to collect the activity of the neuron around the onset of the targeted task event for multiple times, then you can create a rastergram or histogram for visually assess the event-related activity of the neuron.

htbGetRas() performs this data alignment process for a given htbDb object. A pair of htbDb objects with spike and event types are used to create an aligned activity packed into a dedicated list variable called htbRas object. You can also use an htbDb object of analog type when you want to align continuous data (e.g., local field potential, electromyography, eye trajectory) instead of intermittent spike timing data. In either case, the spike/analog database and event database must have been recorded in the same session with completely identical storing configuration. Otherwise, resulting alignment of the data does not make sense since htbGetRas() has no capability in detecting temporal offset or mismatch between provided databases.

Value

An htbRas object.

Examples

alignment <- list(CUEON_L = c(-1500, 2000), CUEON_R = c(-1500, 2000))
incld <- list(TRIALSTART = c(-2000, 0), TRIALEND = c(0, 2000))
excld <- list(ERROR = c(0, 2000))

## Not run: 
db_sp <- htbGetDb("spike.htb")
db_ev <- htbGetDb("event.htb")
ras <- htbGetRas(db_sp, db_ev, alignment,
  incld = incld, excld = excld)

## End(Not run)

keimochizuki/htb documentation built on June 9, 2025, 10:03 p.m.