Dcoef-methods: Dcoef
In sheng-liu/smt: Single Molecule Tracking

Description Usage Arguments Details Value Examples

Caclulate diffusion coefficient (Dcoef) for trajecotries.

1
2
3

Dcoef( MSD=NULL,trackll=NULL,dt=6,filter=c(min=7,max=Inf),rsquare=0.8,resolution=0.107,
       binwidth=NULL,method=c("static","percentage","rolling.window"),
       plot=F,output=F,t.interval=0.01,profile=NULL)

`MSD`	Mean Square Displacement calculated using msd() function. Either MSD or trackll can be passed into Dcoef for calculation of diffusion coefficient.
`trackll`	Track list output from readDiatrack().
`dt`	Time intervals.
`filter`	a vector specifies the minimum and max length of trajecotries to be analyzed. Take only trajectories that has number of frames greater than (>=) min and less than (<) max.
`rsquare`	rsquare filter on Dcoef results. Default to be 0.8. Set value to 0 if rsquare filter is not desired.
`resolution`	ratio of pixel to µM.
`binwidth`	binwidth used for histogram. Default NULL, automatically assign binwidth.
`method`	"static", uses time lags 2~5 to calculate diffusion coefficient; "percentage", uses (tierd) percentage (default 0.25) of time lags (see Details). "rolling.window", time lags uses for Dcoef follows a rolling window with specified window size (default 4).
`plot`	A parameter for plotting. Default FALSE, no plot; If TRUE, automatically plots "histogram" with count information, binwidth can be set through parameter binwidth; as well as "density" with density/frequency.
`output`	An Logical indicate if output should be generated. See Values for detail.
`t.interval`	time interval between frames, default 0.010 s (10ms).
`profile`	Location of preference file. By default (NULL), it is stored at : system.file("extdata","PREF","profile.csv",package="smt"). User can provide preference file by specifying the location of the file, e.g. profile="/Users/shengliu/Desktop/profile.csv".
`lag.start`	time lag used as start of dt for compute Dcoef. Default 2.
`lag.end`	Time lag used as end of dt for compute Dcoef. Default 2.

Generic parameters (parameter applied to all methods, such as resolution etc) are set in the function. Method dependent parameters (such as lag.start, lag.end for method = "static"), are stored in profile.csv in PREF folder under extdata. To change preference parameter, can either programably or manually go to folder system.file("extdata","PREF","profile.csv",package="smt"), and change the profile.csv.

method for calculating Dcoef:

static stabilize the number of time lags used for fitting using time lag 2~ 5 despite the total time lags measured.

percentage "percentage", uses (tierd) percentage (default 0.25) of time lags.

[,1]	TrackLength	Percentage	TimeLagsForFitting
[,2]	31~	0.25	2~5-2~7
[,3]	22~30	0.25	2~5-2~7
[,4]	15~21	0.4	2~5-2~7
[,5]	10~15	0.6	2~5-2~7
[,6]	7~9	1	2~5-2~7

rolling.window time lags uses for Dcoef follows a rolling window with specified window size (default 4).

Dcoef A list of Dcoef for each file in trackll.
PDF Log.Dcoef histogram fitted with density curve, when plot = TRUE.
csv Dcoef output in csv format, when output = TRUE.

# compare files
folder=system.file("extdata","SWR1",package="smt")
trackll=readDiatrack(folder)
MSD=msd(trackll=trackll)
Dcoef(MSD=MSD,method="static",plot=TRUE)

# compare folders
folder1=system.file("extdata","SWR1",package="smt")
folder2=system.file("extdata","HTZ1",package="smt")
trackll2=compareFolder(c(folder1,folder2))
Dcoef(trackll=trackll2,method="percentage",plot=TRUE)
Dcoef(trackll=trackll2,method="rolling.window",plot=TRUE)