calculateCPDs: Calculates the copies per droplet

In bgbrink/dropClust: Clustering algorithm for ddPCR data

Description

This function takes the results of the clustering and calculates the actual counts per target, as well as the counts per droplet (CPD) for each marker.

Usage

calculateCPDs(results, template = NULL, constantControl = NULL)

Arguments

results	The result of the ddPCRclust algorithm.
template	The parsed dataframe containing the template.
constantControl	The constant refrence control, which should be present in each reaction. It is used to normalize the data.

Value

A list of lists, containing the counts for empty droplets, each marker with both total droplet count and CPD, and total number of droplets, for each element of the input list respectively.

Examples

# Read files
exampleFiles <- list.files(paste0(find.package('ddPCRclust'), '/extdata'), full.names = TRUE)
files <- readFiles(exampleFiles[3])
# To read all example files uncomment the following line
# files <- readFiles(exampleFiles[1:8])

# Read template
template <- readTemplate(exampleFiles[9])

# Run ddPCRclust
result <- ddPCRclust(files, template)

# Calculate the CPDs
markerCPDs <- calculateCPDs(result, template$template)

bgbrink/dropClust documentation built on Nov. 7, 2019, 12:18 p.m.