PhIPData

The PhIPData class is used to store experimental results from phage-immunoprecipitation sequencing (PhIP-set) experiments in a matrix-like container.

Building on the RangedSummarizedExperiment class, PhIPData contains all of functionality of SummarizedExperiments and includes additional operations to facilitate analysis with PhIP-seq data. Like SummarizedExperiments, a key feature of PhIPData is the coordination of metadata when subsetting PhIPData objects. For example, if you wanted to examine experimental data for peptides from one particular virus, you can subset the experimental data and the associated peptide annotation with one command. This ensures all metadata (for samples, peptides, etc.) remain synced with the experimental data throughout analysis.

Installation

We recommend installing the stable release version of PhIPData in Bioconductor. This can be done using BiocManager:

if (!require("BiocManager"))
    install.packages("BiocManager")
    
BiocManager::install("PhIPData")

To load the package:

library(PhIPData)

Components of a PhIPData Object

As reflected in the figure below, the structure of a PhIPData object is nearly identical to the structure of a SummarizedExperiment/RangedSummarizedExperiment object.

Each object contains at least three assays of data. These assays are:

• counts: matrix of raw read counts,
• logfc: matrix of log10 estimated fold-changes (in comparison to negative control samples),
• prob: matrix of probabilities (p-values or posterior probabilities) associated with whether a sample shows an enriched antibody response to the particular peptide.

The rows of a PhIPData object represent peptides of interest and the columns represent samples. Sample and peptide metadata are stored in DataFrames. Each row of the metadata DataFrame specifies the peptide/sample, and the columns represent different features associated with the peptides/samples.

In addition to sample- and peptide-specific metadata, experimental metadata such as associated papers, experimental parameters, sequencing dates, etc. are stored in a list-like component named metadata.

Schematic of a PhIPData object. Commands used to access each component of the object are listed underneath its visual representation. Code in black indicates functions specific to `PhIPData` objects while functions in red extend `SummarizedExperiment` functions. Here, `pd` is a generic `PhIPData` object.

Example Use

For an example of how to use PhIPData objects, please see the package vignette.