dbscan_combination {dPCP}

Test eps and minPts combinations for DBSCAN analysis

Description

This function tests all combinations of eps and minPts for DBSCAN analysis of reference samples indicated in refID. The results are represented in scatterplots exported to a pdf file.

Usage

dbscan_combination(
  refID,
  system = NULL,
  file.location = ".",
  reference.quality = 0.5,
  eps = c(120, 150, 180, 200),
  minPts = c(20, 50, 80, 100)
)

Arguments

refID

a string or a character vector of chipID (Thermo Fisher) or the complete file name with the extension (Bio-Rad) of reference sample(s) to be analysed.

system

character. The name of digital PCR system used to generate the data. It must be either Thermo Fisher or Bio-Rad. Abbreviations are also accepted.

file.location

character. Full path name to reference and sample files location. The default corresponds to the working directory, (getwd). Tilde expansion (see (path.expand)) is performed.

reference.quality

numeric. Between 0 and 1. Quality threshold to subset the data (just for Thermo Fisher). If different thresholds have to be applied to various reference samples, a vectror of the same length of refID has to be provided.

eps

a numeric vector of values to be tested. Maximum distance between elements within a cluster in a DBSCAN analysis. See also dbscan.

minPts

a numeric vector of values to be tested. Number of minimum elements to assemble a cluster in a DBSCAN analysis. See also dbscan.

Value

A pdf file containing the scatterplots of DBSCAN analysis performed with all combinations of eps and minPts. Each reference generates a different pdf file.

Examples

library(dPCP)

#Find path of sample table and location of reference and input files
sampleTable <- system.file("extdata", "Template_sampleTable.csv",
                     package = "dPCP")

fileLoc <- system.file("extdata", package = "dPCP")

dbscan_combination("dilution20200313_B01_Amplitude.csv",
                   file.location = fileLoc, system = "bio-rad",
                   eps = c(150, 160, 180, 190), minPts = c(80, 100, 120))

unlink("dilution20200313_B01_Amplitude.pdf")