wsaPreProcessing: Data preprocessing for wound scratch assay (WSA).

Description Usage Arguments Value Author(s) References Examples

View source: R/all_functions_v8.R

Description

This function allows filtering of cells and preprocessing of the trajectory data from wound scratch assay (WSA) experiments.

Usage

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wsaPreProcessing(
  object,
  PixelSize = 1.24,
  TimeInterval = 10,
  FrameN = NULL,
  imageH = 1500,
  woundH = 600,
  upperE = 400,
  lowerE = 1000,
  mar = 75,
  clearW = TRUE,
  ExpName = NULL
)

Arguments

object

CellMig class object.

PixelSize

A numeric value of the physical size of a pixel.

TimeInterval

A numeric value of the time elapsed between successive frames in the time-lapse stack.

FrameN

A numeric value of the number of frames. Default is NULL

imageH

A numeric value of the image height.

woundH

A numeric value of the image height.

upperE

A numeric value of the upper edge of the wound.

lowerE

A numeric value of the lower edge of the wound.

mar

A numeric value of the margin to be used to narrow the clearing zone inside the zone.

clearW

A logical vector that allows removing the cells within the wound. Default is TRUE.

ExpName

string, name of the experiment. Can be NULL

Value

An CellMig class object with filtered, annotated and preprocessed data.

Author(s)

Salim Ghannoum salim.ghannoum@medisin.uio.no

References

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

Examples

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WSADataset <- get(data(WSADataset))
wasDF=WSADataset[seq(1,30,by=1),]
wsaTD <- CellMig(wasDF)
wsaTD <- wsaPreProcessing(wsaTD,FrameN=20)

ocbe-uio/CellMigRation documentation built on Dec. 26, 2021, 10:19 p.m.