Installation | Introduction | Components of a PhIPData Object | Accessing and modifying components of PhIPData object | Assays | Peptide metadata | Sample metadata | Experimental metadata | Common operations on PhIPData objects | Subsetting | PhIPData summaries | Using template libraries | Using aliases | Coercion from PhIPData to other containers | sessionInfo()
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:
PhIPData_1.21.0.tar.gz
PhIPData_1.21.0.zip(r-4.7-any)PhIPData_1.21.0.zip(r-4.6-any)PhIPData_1.21.0.zip(r-4.5-any)
PhIPData_1.21.0.tgz(r-4.6-any)PhIPData_1.21.0.tgz(r-4.5-any)
PhIPData_1.21.0.tar.gz(r-4.7-any)PhIPData_1.21.0.tar.gz(r-4.6-any)
PhIPData_1.21.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
PhIPData/json (API)
| # 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)
infrastructuredatarepresentationsequencingcoverage
Last updated from:6c7acec55d. Checks:8 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 164 | ||
| linux-devel | NOTE | 332 | ||
| source / vignettes | OK | 244 | ||
| linux-release | NOTE | 352 | ||
| macos-release | NOTE | 214 | ||
| macos-oldrel | NOTE | 259 | ||
| windows-devel | NOTE | 234 | ||
| windows-release | NOTE | 217 | ||
| windows-oldrel | NOTE | 233 | ||
| wasm-release | OK | 122 |
Exports:assay<-assays<-countscounts<-deleteAliasgetAliasgetBeadsNamegetLibrarylibrarySizelistLibrarylogfclogfc<-makeLibrarypeptideInfopeptideInfo<-PhIPDataprobprob<-propReadsremoveLibrarysampleInfosampleInfo<-setAliassetBeadsNamesubsetBeads
Dependencies:abindaskpassBiobaseBiocFileCacheBiocGenericsbitbit64blobcachemclicpp11curlDBIdbplyrDelayedArraydplyredgeRfastmapfilelockgenericsGenomicRangesgluehttr2IRangeslatticelifecyclelimmalocfitmagrittrMatrixMatrixGenericsmatrixStatsmemoiseopensslpillarpkgconfigpurrrR6rlangRSQLiteS4ArraysS4VectorsSeqinfoSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselectutf8vctrswithrXVector
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 |