OAtools

Overview

OAtools is an R package for analyzing OpenArray gene expression experiments motivated by a desire to support open-source and shareable data analyses in public health and research environments.

OAtools offers a public API for the following:

• converting run data into ergonomic Bioconductor class objects
• analyzing OpenArray experiments by fitting logistic models to PCR curves
• rendering pre-packaged plots to visualize experiment outcomes
• generating an HTML document summarizing run results for reporting

Installation

You can install the development version of OAtools from the UW Virology NGS GitHub:

# Install the devtools package
install.packages("devtools")

# Install the development version of OAtools from the UW Virology NGS GitHub
devtools::install_github(
    repo = "uwvirology-ngs/OAtools", 
    dependencies = TRUE, 
    build_vignettes = TRUE
)

Documentation

The full documentation for OAtools may be found in the package vignette. Once OAtools is installed, the vignette is accessible by running the following command in the R console:

browseVignettes(package = "OAtools")

Example

Here we demonstrate a minimal example of the OAtools workflow. Please refer to the package vignette for more comprehensive documentation.

Importing Run Data

Once data has been exported in excel format from QuantStudio 12K Flex Software, we can load the experiment into a SummarizedExperiment container.

# save filepath to example OpenArray gene expression run data
path = system.file(
    "extdata", 
    "oa_gene_expression_1.xlsx", 
    package = "OAtools"
)

# transform the run data into a SummarizedExperiment
se <- excelToSE(excel_path = path)

Analyzing PCR with logistic regressions

Next, we run an optimizer to fit logistic regressions to each amplification curve and use the resulting model equation to derive PCR results. A pre-made key defines thresholds that separate curves into positive and negative results.

# optimize model curves to each PCR reaction
se <- computeModels(
    se = se,
    assay_name = "fluo_reporter"
)

# save filepath to assay target key
key_path = system.file(
    "extdata", 
    "target_threshold_key.xlsx", 
    package = "OAtools"
)

# assign a PCR result according to the key
se <- determinePCRResults(
    se = se, 
    key_path = key_path
)

Communicating the Results

Finally, we dynamically generate an HTML run report to summarize the outcome of the experiment.

# generate a .html report from the run data
generateReport(se = se)

Interoperability

OAtools supports interoperability with the twin packages ReadqPCR and NormqPCR, which normalize RT-qPCR gene expression data from platforms like OpenArray. Refer to the package vignette for example code or the official NormqPCR Documentation for normalization workflows.

Shiny app

To invoke the built-in Shiny GUI for running OAtools, run the following in the R console:

shiny::runApp(buildApp())

Getting Help

For feature suggestions or bug reports, please file an issue on the project GitHub