What this covers | Cross-sectional: one sample per subject | Longitudinal: multiple samples per subject | Key points
Package: phiperio 0.5.0
phiperio: PhIP-Seq Data Import and Validation Tools
Provides utilities to import, validate, and manage PhIP-Seq datasets, including standardized conversion pipelines, data checks, and access to cached peptide metadata.
Authors:
phiperio_0.5.0.tar.gz
phiperio_0.5.0.zip(r-4.7)phiperio_0.5.0.zip(r-4.6)phiperio_0.5.0.zip(r-4.5)
phiperio_0.5.0.tgz(r-4.6-any)phiperio_0.5.0.tgz(r-4.5-any)
phiperio_0.5.0.tar.gz(r-4.7-any)phiperio_0.5.0.tar.gz(r-4.6-any)
phiperio_0.5.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
phiperio/json (API)
| # Install 'phiperio' in R: |
| install.packages('phiperio', repos = c('https://polymerase3.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/polymerase3/phiperio/issues
Pkgdown/docs site:https://polymerase3.github.io
Last updated from:cd3f886b5d (on main). Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 154 | ||
| source / vignettes | OK | 196 | ||
| linux-release-x86_64 | OK | 163 | ||
| macos-release-arm64 | OK | 90 | ||
| macos-oldrel-arm64 | OK | 117 | ||
| windows-devel | OK | 108 | ||
| windows-release | OK | 107 | ||
| windows-oldrel | OK | 109 | ||
| wasm-release | OK | 124 |
Exports:add_existconvert_legacyconvert_standardcreate_dataexpand_dataexport_parquetget_countsget_example_pathget_metaget_peptide_libraryload_example_data
Dependencies:blobchkclicpp11DBIdbplyrdplyrduckdbgenericsgluelifecyclemagrittrpillarpkgconfigpurrrR6rlangstringistringrtibbletidyrtidyselectutf8vctrswithryaml
Importing legacy PhIP-Seq data (convert_legacy)
Last update: 2026-02-04
Started: 2026-02-04
Importing multiple files with phiperio
Overview | 1. Create a bunch of example files | 2. Inspect one file so you know what’s inside | 3. Import all files in one call | 4. Derive run_id and plate_id from sample_id | Summary
Last update: 2026-02-04
Started: 2026-02-04
Importing cross-sectional and longitudinal tidy data with phiperio
Overview | Key concepts (read first) | Cross-sectional workflow (simpler) | Longitudinal workflow (subjects with multiple samples) | Tips and gotchas | Using the built-in example
Last update: 2026-02-04
Started: 2026-02-04
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Ensure an existence flag (all ones) on 'data_long' | add_exist |
| Close phip_data connections | close.phip_data |
| Convert legacy Carlos-style input to a modern *phip_data* object | convert_legacy |
| Convert raw PhIP-Seq output into a 'phip_data' object | convert_standard |
| Construct a *phip_data* object | create_data |
| Expand to a full 'sample_id * peptide_id' grid | expand_data |
| Export a phip_data Table to Parquet | export_parquet |
| Retrieve the main PhIP-Seq counts table | get_counts |
| Path to example PhIP-Seq datasets shipped with phiperio | get_example_path |
| Retrieve the metadata list | get_meta |
| Retrieve the peptide metadata table into DuckDB, forcing atomic types | get_peptide_library |
| Load Example PhIP-Seq Dataset as <phip_data> | load_example_data |
| Merge or join a 'phip_data' object | merge.phip_data |
| dplyr joins for 'phip_data' | anti_join.phip_data full_join.phip_data inner_join.phip_data left_join.phip_data phip_data_join right_join.phip_data semi_join.phip_data |
