PhIPData

PhIPData defines an S4 class for phage-immunoprecipitation sequencing (PhIP-seq) experiments that coordinates metadata with experimental data in analyses.

Key Features:

• S4 Class Infrastructure: PhIPData builds upon the RangedSummarizedExperiment class to structure PhIP-seq experimental data.
• Metadata Coordination: PhIPData enables coordination of metadata with experimental data in analyses.
• Beads-Only Sample Handling: PhIPData provides specialized methods to subset and identify beads-only samples.
• Virus Alias Subsetting: PhIPData provides specialized methods to subset objects using virus aliases.
• Peptide Library Integration: PhIPData provides specialized methods to use existing peptide libraries to populate object parameters.

Scientific Applications:

• PhIP-Seq Experiment Management: PhIPData supports organization and analysis of phage-immunoprecipitation sequencing experiments through structured data containers.

Methodology:

PhIPData extends the RangedSummarizedExperiment class with specialized S4 methods for PhIP-seq data operations including subsetting by virus aliases and identifying beads-only samples.