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scbursts (version 1.6)

Single Channel Bursts Analysis

Description

Provides tools to import and export from several existing pieces of ion-channel analysis software such as 'TAC', 'QUB', 'SCAN', and 'Clampfit', implements procedures such as dwell-time correction and defining bursts with a critical time, and provides tools for analysis of bursts, such as tools for sorting and plotting.

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Version

Install

install.packages('scbursts')

Monthly Downloads

152

Version

1.6

License

LGPL-2.1

Maintainer

Blair Drummond

Last Published

July 6th, 2019

Functions in scbursts (1.6)

bursts.space_out

Artificially add amount of time between bursts (in absence of recording information).
segment.count_closed

Extract number of closed dwells. In the case of subconductive states, a dwell is only closed if the conductance is exactly zero.
cplot.popen_ts

Plot Time Series (ts) of P(Open).
segment.modify_conductance

Transform the conductance states according to a user-defined function of conductance level.
dwt.read

Read a .dwt file.
segment.count_dwells

Extract number of dwells in segment.
bursts.conductance_states

Return a list of all the (sub)conductance states.
segment.name

Extract name from segment.
segment.dwells_by_conductance_range

Extract dwells in conductance range. lower <= x <= upper
bursts.subconductance_as

Imposes a fixed conductance level (0 or 1) to all dwells with subconductance levels to each segment in a burst
segment.verify

Detect misrecorded data.
util.basename

Remove suffix and path from filename.
segment.create

Create a "segment" object
evt.write

Write bursts to a .evt file.
segment.conductance_states

Return a list of all the (sub)conductance states.
segment.closed_dwells

Extract closed dwells.
evt.to_dwells

Calculate pulse lengths. Converts transition times to dwell durations.
segment.count_open

Extract number of open dwells. In the case of subconductive states, count the number of non-zero states.
dwt.write

Write a dwt file to disk. Writes DOS line endings. Dwells are in milliseconds
clampfit.read

Read a .xlsx file output from clampfit
cplot.conductance_hist

Histogram of Conductance States
bursts.modify_conductance

Transform the conductance states according to a user-defined function of conductance level.
segment.impose_deadtime

Imposes a deadtime to a segment by removing any dwell that is shorter than the deadtime.
scan.read

Read a scan results text file. scan.read returns a 1 segment list Reads in scan results and puts them in the same format as the output of dwt.read. See 'dwt', and 'segment' for more information.
evt.extract_header

Extract header from evt file.
bursts.pcloseds

Return pcloseds of every burst.
cplot.log_root_axes

Add log-root axes to histogram plot
bursts.remove_first_and_last

Remove the first and last burst from the list.
bursts.recombine

Combine bursts into one recording (with obvious spaces between them).
hst.read

Read a MIL ".hst" file to a table.
hst.extract_header

Extract header from hst file.
bursts.select

From a list of bursts, extract those that interest you by passing a selecting function.
cplot.pclosed_ts

Plot Time Series (ts) of P(Closed).
segment.check_subconductance

Check if segment contains subconductive states
evt.from_dwells

Converts dwell durations to absolute transition times.
segment.popen

Calculate empirical P(Open) of a segment. (A state is considered open if the conductance is non-zero)
evt.read

Read a .evt file to a table. Times are in seconds
segment.consecutives_to_dwells

Collapses a segment into dwells with alternating conductance levels.
segment.pconductance

Calculate empirical P(Lower <= Conductance <= Upper) of a segment.
risetime.correct_gaussian

Undo the effect of the gaussian filter.
segment.dwells_by_conductance

Extract dwells in conductance range. lower <= x <= upper
segment.duration

Get duration of a segment.
hst.write

Write bursts to a log10(ms)-sqrt(Frequency) .hst file from open and closed tables.
segment.seg

Extract segment number from segment.
segment.open_dwells

Extract open dwells. (Any conductance greater than zero)
segment.copy

Copy a segment
segment.pclosed

Calculate empirical P(Closed) of a segment.
segment.pconductance_range

Calculate empirical P(Lower <= Conductance <= Upper) of a segment.
segment.subconductance_as

Imposes a fixed conductance level (0 or 1) to all dwells with subconductance levels.
segment.start_time

Extract start_time from segment.
bursts.check_subconductance

Check if segment contains subconductive states
bursts.copy

Copy a list of bursts (by value)
bursts.popens

Return popens of every burst.
bursts.get_gaps

Get the gaps between bursts.
bursts.defined_by_tcrit

Divide a recording into bursts defined by a critical time.
bursts.impose_deadtime

Imposes a deadtime to each segment in a burst.
bursts.start_times_update

(DON'T USE THIS) Fix meta-data of bursts.
bursts.sort

Order a list of bursts by some function. For instance, popen.