Package: PhIPData 1.21.0

Athena Chen

PhIPData: Container for PhIP-Seq Experiments

PhIPData defines an S4 class for phage-immunoprecipitation sequencing (PhIP-seq) experiments. Buliding upon the RangedSummarizedExperiment class, PhIPData enables users to coordinate metadata with experimental data in analyses. Additionally, PhIPData provides specialized methods to subset and identify beads-only samples, subset objects using virus aliases, and use existing peptide libraries to populate object parameters.

Authors:Athena Chen [aut, cre], Rob Scharpf [aut], Ingo Ruczinski [aut]

PhIPData_1.21.0.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
PhIPData/json (API)
NEWS

# Install 'PhIPData' in R:

install.packages('PhIPData', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/athchen/phipdata/issues

On BioConductor:PhIPData-1.21.0(bioc 3.24)PhIPData-1.20.0(bioc 3.23)

infrastructure datarepresentation sequencing coverage

5.32 score 7 stars 1 packages 7 scripts 332 downloads 25 exports 57 dependencies

Last updated from:6c7acec55d. Checks:8 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	182
linux-devel-x86_64	NOTE	305
source / vignettes	OK	232
linux-release-x86_64	NOTE	364
macos-release-arm64	NOTE	181
macos-oldrel-arm64	NOTE	191
windows-devel	NOTE	277
windows-release	NOTE	266
windows-oldrel	NOTE	240
wasm-release	OK	125

Exports:assay<-assays<-counts counts<-deleteAlias getAlias getBeadsName getLibrary librarySize listLibrary logfc logfc<-makeLibrary peptideInfo peptideInfo<-PhIPData prob prob<-propReads removeLibrary sampleInfo sampleInfo<-setAlias setBeadsName subsetBeads

Dependencies:abind askpass Biobase BiocFileCache BiocGenerics bit bit64 blob cachem cli cpp11 curl DBI dbplyr DelayedArray dplyr edgeR fastmap filelock generics GenomicRanges glue httr2 IRanges lattice lifecycle limma locfit magrittr Matrix MatrixGenerics matrixStats memoise openssl pillar pkgconfig purrr R6 rappdirs rlang RSQLite S4Arrays S4Vectors Seqinfo SparseArray statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect utf8 vctrs withr XVector

PhIPData: A Container for PhIP-Seq Experiments

Athena Chen, Rob Scharpf, and Ingo Ruczinski

Rendered fromPhIPData.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2022-02-05
Started: 2021-01-06

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Using aliases to subset virus data	aliases deleteAlias getAlias setAlias
Defining how beads-only samples are encoded.	defineBeads getBeadsName setBeadsName
Calculate total read counts for each sample.	librarySize
Peptide libraries	getLibrary listLibrary makeLibrary peptideLibraries removeLibrary
The PhIPData class	.PhIPData PhIPData PhIPData-class
Accessing and Modifying Information in PhIPData objects	assay<-,PhIPData,character-method assay<-,PhIPData,missing-method assay<-,PhIPData,numeric-method assays<-,PhIPData,list-method assays<-,PhIPData,SimpleList-method counts,PhIPData-method counts<-,PhIPData-method logfc logfc,PhIPData-method logfc<- logfc<-,PhIPData-method peptideInfo peptideInfo,PhIPData-method peptideInfo<- peptideInfo<-,PhIPData-method PhIPData-methods prob prob,PhIPData-method prob<- prob<-,PhIPData-method sampleInfo sampleInfo,PhIPData-method sampleInfo<- sampleInfo<-,PhIPData-method
Proportion of sample reads	propReads
Subset beads-only samples	subsetBeads