subtracksByTime: Extract Subtracks Starting at a Specific Time

In celltrackR: Motion Trajectory Analysis

Extract Subtracks Starting at a Specific Time

Description

Obtain all subtracks of i steps (i+1 positions) starting at a given timepoint t.

Usage

subtracksByTime(X, t, i = 1, epsilon = 1e-04, tlo = t, thi = t)

Arguments

X	Tracks object to obtain subtracks from.
t	Timepoint at which the subtracks should start. This value is ignored if tlo and thi are specified, see below.
i	Subtrack length (in number of steps). Set this to NULL to obtain subtracks of varying length but within a specified interval [tlo, thi] (see below).
epsilon	Small error allowed when comparing timepoints because of numerical inaccuracies, see details. Timepoints in tracks are returned if they are within [tlo-epsilon, thi+epsilon].
tlo, thi	Interval specifying the timepoints to be returned. By default, these are not used and tracks starting at timepoint t with exactly i steps are returned; see details.

Details

If i is specified, the given t is retrieved for all tracks in X that contain that timepoint, and any subtracks starting from that time that have exactly i steps are returned. For numerical reasons, timepoints in the data are allowed to deviate a small amount epsilon from t (because otherwise, equal timepoints can seem unequal because of very small deviations).

If i is set to NULL, subtracks are returned with all timepoints lying in the interval [ tlo - epsilon, thi + epsilon ]. These subtracks do NOT have to be of equal length.

Value

A tracks object is returned which contains all the subtracks of any track in the input tracks object that consist of exactly 'i' segments and start at the given timepoint t, OR a tracks object with all the timepoints of any track in the input tracks object that are between tlo and thi.

See Also

subtracks to extract all subtracks of a given length, prefixes to extract all subtracks of a given length starting from the first coordinate in each track, selectSteps to extract single steps starting at a fixed timepoint from a subset of trackids, and timePoints to return all timepoints occurring in the dataset.

Examples

## Get all the single steps (i=1) starting at the third timepoint in the T cell tracks.
subT <- subtracksByTime( TCells, timePoints(TCells)[3], 1 )

## These all have the same number of steps:
sapply( subT, nrow )

## Or set i to NULL and return all subtracks within the five first timepoints:
subT2 <- subtracksByTime( TCells, NULL, i = NULL,
  tlo = timePoints( TCells )[1], thi = timePoints( TCells )[5] )

## These are not all the same length:
sapply( subT2, nrow )

celltrackR documentation built on March 21, 2022, 5:06 p.m.