Package: PhIPData 1.13.0

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]

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PhIPData.pdf |PhIPData.html✨
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-1.13.0(bioc 3.20)PhIPData-1.12.0(bioc 3.19)

bioconductor-package

25 exports 0.82 score 65 dependencies 1 dependents

Last updated 2 months agofrom:a36243067a

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 crayon curl DBI dbplyr DelayedArray dplyr edgeR fansi fastmap filelock generics GenomeInfoDb GenomeInfoDbData GenomicRanges glue httr IRanges jsonlite lattice lifecycle limma locfit magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pillar pkgconfig plogr purrr R6 Rcpp rlang RSQLite S4Arrays S4Vectors SparseArray statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect UCSC.utils utf8 vctrs withr XVector zlibbioc

PhIPData: A Container for PhIP-Seq Experiments

Athena Chen, Rob Scharpf, and Ingo Ruczinski

Rendered fromPhIPData.Rmdusingknitr::rmarkdownon Jun 30 2024.

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