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Type: Package
Title: Invasion Correction
Version: 0.1
Date: 2017-02-20
Author: Marcus Rosenblatt
Maintainer: Marcus Rosenblatt <marcus.rosenblatt@fdm.uni-freiburg.de>
Description: The correction is achieved under the assumption that non-migrating cells of the essay approximately form a quadratic flow profile due to frictional effects, compare law of Hagen-Poiseuille for flow in a tube. The script fits a conical plane to give xyz-coordinates of the cells. It outputs the number of migrated cells and the new corrected coordinates.
License: GPL-3
Depends: lattice, stats, utils
LazyData: TRUE
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2017-02-23 16:42:01 UTC; marcus
Repository: CRAN
Date/Publication: 2017-02-23 17:58:01

Correct invasion data by conical plane

Description

Correct z-component of a 3D collagen invasion essay. The correction is achieved under the assumption that non-migrating cells of the essay approximately form a quadratic flow profile due to frictional effects, compare law of Hagen-Poiseuille for flow in a tube.

Usage

correctByConicalPlane(filename, nrfits = 1000, threshold = -30,
  plot = FALSE, write_csv = TRUE)

Arguments

filename

Name of data file in csv format. It should contain columns "Pos_X", "Pos_Y" and "Pos_Z".

nrfits

Numeric, Number of randomly chosen starting points for the optimization. Choose lower values for speeding up computational time. Choose higher values for more reliable optimization results.

threshold

Numeric, A threshold for counting cells as being invaded or not. When cells move towards negative z-direction, threshold should be negative.

plot

Boole, if TRUE exemplary 3D plots before and after the correction are plotted

write_csv

if TRUE resulting corrected values are saved as a csv file

Value

Data.frame containing input positions, corrected z-positions as well as number and percentage of invaded cells.

Author(s)

Marcus Rosenblatt, marcus.rosenblatt@fdm.uni-freiburg.de

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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