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 1.2.0 Index]