# Container for PhIP-Seq Experiments

## Documentation for package ‘PhIPData’ version 1.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

.PhIPData | The PhIPData class
aliases | Using aliases to subset virus data
assay<--method | Accessing and Modifying Information in PhIPData objects
assays<--method | Accessing and Modifying Information in PhIPData objects
counts-method | Accessing and Modifying Information in PhIPData objects
counts<--method | Accessing and Modifying Information in PhIPData objects
defineBeads | Defining how beads-only samples are encoded.
deleteAlias | Using aliases to subset virus data
getAlias | Using aliases to subset virus data
getAliasPath | Using aliases to subset virus data
getBeadsName | Defining how beads-only samples are encoded.
getLibrary | Peptide libraries
getLibraryPath | Peptide libraries
librarySize | Calculate total read counts for each sample.
logfc | Accessing and Modifying Information in PhIPData objects
logfc-method | Accessing and Modifying Information in PhIPData objects
logfc<- | Accessing and Modifying Information in PhIPData objects
logfc<--method | Accessing and Modifying Information in PhIPData objects
makeLibrary | Peptide libraries
peptideInfo | Accessing and Modifying Information in PhIPData objects
peptideInfo-method | Accessing and Modifying Information in PhIPData objects
peptideInfo<- | Accessing and Modifying Information in PhIPData objects
peptideInfo<--method | Accessing and Modifying Information in PhIPData objects
peptideLibraries | Peptide libraries
PhIPData | The PhIPData class
PhIPData-class | The PhIPData class
PhIPData-methods | Accessing and Modifying Information in PhIPData objects
prob | Accessing and Modifying Information in PhIPData objects
prob-method | Accessing and Modifying Information in PhIPData objects
prob<- | Accessing and Modifying Information in PhIPData objects
prob<--method | Accessing and Modifying Information in PhIPData objects
propReads | Proportion of sample reads
sampleInfo | Accessing and Modifying Information in PhIPData objects
sampleInfo-method | Accessing and Modifying Information in PhIPData objects
sampleInfo<- | Accessing and Modifying Information in PhIPData objects
sampleInfo<--method | Accessing and Modifying Information in PhIPData objects
setAlias | Using aliases to subset virus data
setAliasPath | Using aliases to subset virus data
setBeadsName | Defining how beads-only samples are encoded.
setLibraryPath | Peptide libraries
subsetBeads | Subset beads-only samples