linkSkippedFrames-methods: linkSkippedFrames
In sheng-liu/sojourner: Statistical analysis of single molecule trajectories

Description Usage Arguments Details Value Examples

link trajectories skipped (or do not appear for) a number of frames

1	linkSkippedFrames(trackll, tolerance, maxSkip, cores = 1)

`tolerance`	Distance tolerance level measured in pixels after the frame skip.
`maxSkip`	Maximum number of frames a trajectory can skip.
`trackll`	A list of track lists.
`cores`	Number of cores used for parallel computation. This can be the cores on a workstation, or on a cluster. Tip: each core will be assigned to read in a file when paralleled.

Given user input for a tolerance level to limit how far the next point after the skip can deviate from the last point in pixel distance and a maximum number of frame skips possible, all trajectories falling within these parameters are automatically linked, renamed, and ordered accordingly. For a maxSkip example, if the maxSkip for a trajectory ending in frame 7 was 3, the next linked trajectory can start up to a maximum frame of 11.

Although not required, in order for the output to have a frame record column (recommended), the input must have one as well.

The naming scheme for each linked track is as follows:

[Last five characters of the file name].[Start frame #].[Length].[Track #]. [# of links]

Track List: [full name of input file]

Track: [Last five characters of the file name].[Start frame].[Length]. [Track].[# of links]. [Index in overall list (will differ from Track # when merging)]

(Note: The last five characters of the file name, excluding the extension, cannot contain '.')

linked trackll

folder=system.file('extdata','SWR1',package='sojourner')
trackll=createTrackll(folder=folder, input=3)
#Basic function call of linkSkippedFrames
trackll.linked <- linkSkippedFrames(trackll, tolerance = 5, maxSkip = 10)