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

Description Usage Arguments Details Value Examples

take in Diatrack (.txt or .mat), ImageJ Particle Tracker (.csv), SLIMfast (.txt), or u-track (.mat) input from a folder to output a list of track lists.

1 2	createTrackll(folder, interact = FALSE, input = 1, ab.track = FALSE, cores = 1, frameRecord = TRUE)

`folder`	Full path output file folder (ensure each folder has files of only one input type).
`interact`	Open interactive menu to choose the desired folder by selecting any file in it and select input type (script will process all files of that type in this folder).
`input`	Input file type (Diatrack .txt file = 1; Diatrack .mat session file = 2; ImageJ .csv file = 3; SLIMfast .txt file = 4; u-track .mat file = 5).
`ab.track`	Use absolute coordinates for tracks.
`cores`	Number of cores used for parallel computation. This can be the cores on a workstation, or on a cluster. Each core will be assigned to read one file when in parallel.
`frameRecord`	Add a fourth column to the track list after the xyz-coordinates for the frame that coordinate point was found (especially helpful when linking frames). Highly recommended to leave on.

(Note: When reading only Diatrack .mat session files (input = 2), intensities will be saved after the frame column)

It is highly advised that the frame record option be left on to preserve the most information, especially when linking frames and when using Utrack. If the frame record option is turned on for reading Diatrack .txt files (input = 1), take note that the frame record is artificially created as consecutive frames after the given start frame. Otherwise, all other data types naturally record the frames of every coordinate point.

The pre-censoring of single-frame tracks is dependent on the tracking software. For highest fidelity track data, use Diatrack (.mat) session files. If the initial creation of the trackll does not have a frame record, future exports and imports of the trackll will only preserve the start frames.

If the cores are set to the maximum number of cores available on the system, the script may return a error after processing all the files. This error is due to the requirement of some systems to have one core open for system functions. This error will not affect the trackll output, but to avoid it, one can input one less than the maximum number of cores available.

The naming scheme for the list of track list is as follows:

Track List: [full name of input file]

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

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

trackll

# Designate a folder and then create trackll from .csv data
folder=system.file('extdata','SWR1',package='sojourner')
trackll = createTrackll(folder=folder, input=3)
# Alternatively, use interact to open file 
# browser and select input data type
# trackll <- createTrackll(interact = TRUE)