podcallDdpcr {PoDCall}R Documentation

Positive Droplet Calling for ddPCR

Description

Wrapper function that provide a complete workflow for the functionality of PoDCall. It takes path to amplitude files and sample sheet (optional), and parameters for setting threshold as input. Calls functions that read in data from files, sets threshold for each channel per well, calculates concentrations and optionally makes scatter plot and histogram for each channel per well. Results are returned as a table, optionally written to file. Plots will be written to file in a results directory if argument plots is set to TRUE.

Usage

podcallDdpcr(dataDirectory,
                    sampleSheetFile=NULL,
                    B=200,
                    Q=9,
                    refwell=1,
                    ch2=TRUE,
                    resultsToFile=FALSE,
                    plots=FALSE,
                    resPath=NULL)

Arguments

dataDirectory

Path to directory containing QuantaSoft amplitude files from one 96 well plate. Since well coordinates are used as identifiers, files in this directory should all be from the same 96 well plate. Furthermore, there can be no other files than the amplitude files from a well plate in the directory.

sampleSheetFile

File (optional) containing sample information from ddPCR experiment. This file must be a comma separated file containing the following columns: Well, Sample, TargetType and Target.

B

The number of permutations used for the Likelihood Ratio Test (default=200)

Q

A parameter for calling outliers (default=9)

refwell

reference well to calculate the shift in baseline (default=1)

ch2

Logical argument to denote channel 2 amplitudes (default=TRUE)

resultsToFile

Should results be written to file(.csv)? (default=FALSE)

plots

Should plots be created and written to file? (default=FALSE)

resPath

Optional argument to provide results directory path (default=NULL)

Value

The function returns a table (data frame) with thresholds, droplet counts, concentration and normalized concentration. The table is optionally written to a .csv-file and plots for both channels per well can be written to files.

Examples


## Paths to data and sample sheet
dataPath <- system.file("extdata", "Amplitudes/", package="PoDCall")
ssPath <- system.file("extdata", "Sample_names.csv", package="PoDCall")

## Run PodCall
podcallResults <- podcallDdpcr(dataDirectory=dataPath,
                                sampleSheetFile=ssPath,
                                B=100)


[Package PoDCall version 1.1.5 Index]