test_panel: Dispersion Test for Spatial Point Pattern in Array dPCR Based...
In dpcR: Digital PCR Analysis

Description Usage Arguments Details Value Note Author(s) References See Also Examples

Performs a test of Complete Spatial Randomness for each plate. This function is a wrapper around quadrat.test function working directly on the objects of adpcr.

1
2
3

test_panel(X, nx = 5, ny = 5, alternative = c("two.sided", "regular",
  "clustered"), method = c("Chisq", "MonteCarlo"), conditional = TRUE,
  nsim = 1999)

`X`	Object of the `adpcr` class containing data from one or more panels.
`nx`	Number of quadrats in the x direction.
`ny`	Number of quadrats in the y direction.
`alternative`	`character` string (partially matched) specifying the alternative hypothesis.
`method`	`character` string (partially matched) specifying the test to use: either `"Chisq"` for the chi-squared test (the default), or `"MonteCarlo"` for a Monte Carlo test.
`conditional`	`logical`. Should the Monte Carlo test be conducted conditionally upon the observed number of points of the pattern? Ignored if method="Chisq".
`nsim`	The number of simulated samples to generate when method="MonteCarlo".

Under optimal conditions, the point pattern of dPCR events (e.g., positive droplet & negative droplets) should be randomly distrubuted over a planar chip. This function verifies this assumption using chi-square or Monte Carlo test. Arrays with non-random patterns should be checked for integrity.

A list of objects of class "htest" with the length equal to the number of plates (minimum 1).

A similar result can be achived by using adpcr2ppp and quadrat.test. See Examples.

Adrian Baddeley, Rolf Turner, Michal Burdukiewcz, Stefan Roediger.

http://www.spatstat.org/

quadrat.test.

many_panels <- sim_adpcr(m = 400, n = 765, times = 1000, pos_sums = FALSE, 
                   n_panels = 5)
test_panel(many_panels)

#test only one plate
test_panel(extract_run(many_panels, 3))

#do test_panel manually
require(spatstat)
ppp_data <- adpcr2ppp(many_panels)
lapply(ppp_data, function(single_panel) quadrat.test(single_panel))