MSD: Mean Square Displacement

In ocbe-uio/cellmigRation: Track Cells, Analyze Cell Trajectories and Compute Migration Statistics

Description

The MSD function automatically computes the mean square displacements across several sequential time intervals. MSD parameters are used to assess the area explored by cells over time.

Usage

MSD(
  object,
  TimeInterval = 10,
  sLAG = 0.25,
  ffLAG = 0.25,
  SlopePlot = TRUE,
  AllSlopesPlot = TRUE,
  FurthPlot = TRUE,
  AllFurthPlot = TRUE,
  export = FALSE,
  ExpName = NULL
)

Arguments

object	CellMig class object, which is a list of data frames resulted from the PreProcessing.
TimeInterval	A numeric value of the time elapsed between successive frames in the time-lapse stack.
sLAG	A numeric value to be used to get the number of lags for the slope fitting. Default is 0.25, which represents 25 percent of the steps.
ffLAG	A numeric value to be used to get the number of lags for the Furth formula fitting. Default is 0.25, which represents 25 percent of the steps.
SlopePlot	A logical vector that allows generating individual plots showing the slope of the mean square displacement of the movement of individual cells. Default is TRUE.
AllSlopesPlot	A logical vector that allows generating a plot showing the slope of the mean square displacement of the movement of all cells. Default is TRUE.
FurthPlot	A logical vector that allows generating individual plots fitting the Furth formula using generalized regression by the Nelder–Mead method simplex method per cell. Default is TRUE.
AllFurthPlot	A logical vector that allows generating a plot fitting the Furth formula using generalized regression by the Nelder–Mead method simplex method for all cells. Default is TRUE.
export	if 'TRUE' (default), exports function output
ExpName	string, anem of the Experiment. Can be NULL

Value

An CellMig class object with a data frame and plots. The data frame is stored in the MSDtable slot.

Author(s)

Salim Ghannoum [e-mail]

References

https://www.data-pulse.com/dev_site/cellmigration/

Examples

data(TrajectoryDataset)
rmDF <- TrajectoryDataset[seq(1,220,by=1), ]
rmTD <- CellMig(rmDF)
rmTD <- rmPreProcessing(rmTD,FrameN=100)
rmTD <- MSD(rmTD, sLAG=0.25, ffLAG=0.25, export=FALSE)

ocbe-uio/cellmigRation documentation built on Dec. 16, 2021, 10:59 p.m.