Package: plyxp 1.1.0
Justin Landis
plyxp: Data masks for SummarizedExperiment enabling dplyr-like manipulation
The package provides `rlang` data masks for the SummarizedExperiment class. The enables the evaluation of unquoted expression in different contexts of the SummarizedExperiment object with optional access to other contexts. The goal for `plyxp` is for evaluation to feel like a data.frame object without ever needing to unwind to a rectangular data.frame.
Authors:
plyxp_1.1.0.tar.gz
plyxp_1.1.0.zip(r-4.5)plyxp_1.1.0.zip(r-4.4)
plyxp_1.1.0.tgz(r-4.4-any)
plyxp_1.1.0.tar.gz(r-4.5-noble)plyxp_1.1.0.tar.gz(r-4.4-noble)
plyxp_1.1.0.tgz(r-4.4-emscripten)
plyxp.pdf |plyxp.html✨
plyxp/json (API)
NEWS
| # Install 'plyxp' in R: |
| install.packages('plyxp', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/jtlandis/plyxp/issues
Pkgdown:https://jtlandis.github.io
- se_simple - Plyxp Simple Example Summarized Experiment
On BioConductor:plyxp-1.1.0(bioc 3.21)plyxp-1.0.0(bioc 3.20)
annotationgenomeannotationtranscriptomics
Last updated 2 months agofrom:90c53d12d6. Checks:OK: 5. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 14 2024 |
| R-4.5-win | OK | Dec 14 2024 |
| R-4.5-linux | OK | Dec 14 2024 |
| R-4.4-win | OK | Dec 14 2024 |
| R-4.4-mac | OK | Dec 14 2024 |
Exports:.assays.assays_asis.cols.cols_asis.rows.rows_asisarrangeassayassay_ctxassay<-assaysassays<-class_DFclass_s4_vctrsclass_vctrscol_ctxcolDatacolData<-colsfiltergroup_bygroup_datagroup_varsmetadatametadata<-mutatenew_plyxpPlySummarizedExperimentplyxpplyxp_pillar_formatpullrow_ctxrowDatarowData<-rowssese<-selectshow_tidysummarisesummarizeSummarizedExperimentungroupuse_show_defaultuse_show_tidyvec_phantomvec_recyclevec_repvec_rep_eachvec_slice
Dependencies:abindaskpassBiobaseBiocGenericsclicpp11crayoncurlDelayedArraydplyrfansigenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehttrIRangesjsonlitelatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslpillarpkgconfigpurrrR6rlangS4ArraysS4VectorsS7SparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrswithrXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| arrange rows or columns of PlySummarizedExperiment | arrange arrange.PlySummarizedExperiment |
| create data.frame | as.data.frame as.data.frame.PlySummarizedExperiment |
| contextual plyxp pronouns | .assays .assays_asis .cols .cols_asis .rows .rows_asis dot-pronouns |
| filter PlySummarizedExperiment | filter filter.PlySummarizedExperiment |
| apply groups to PlySummarizedExperiment | group_by group_by.PlySummarizedExperiment ungroup.PlySummarizedExperiment |
| get grouping data | group_data group_data.PlySummarizedExperiment ungroup |
| get PlySummarizedExperiment grouping Variables | group_vars group_vars.PlySummarizedExperiment |
| Mutate a PlySummarizedExperiment object | mutate mutate.PlySummarizedExperiment |
| SummarizedExperiment Shell Object | new_plyxp PlySummarizedExperiment PlySummarizedExperiment-class |
| Modify SummarizedExperiment Object | plyxp |
| plyxp contexts | assay_ctx cols col_ctx plyxp-context rows row_ctx |
| extract data from object | pull pull.PlySummarizedExperiment |
| PlySummarizedExperiment Methods | assay,PlySummarizedExperiment,character-method assay,PlySummarizedExperiment,missing-method assay,PlySummarizedExperiment,numeric-method assay<-,PlySummarizedExperiment,character-method assay<-,PlySummarizedExperiment,missing-method assay<-,PlySummarizedExperiment,numeric-method assays,PlySummarizedExperiment-method assays<-,PlySummarizedExperiment,list-method assays<-,PlySummarizedExperiment,SimpleList-method colData,PlySummarizedExperiment-method colData<-,PlySummarizedExperiment,DataFrame-method colData<-,PlySummarizedExperiment,NULL-method PlySummarizedExperiment-methods rowData,PlySummarizedExperiment-method rowData<-,PlySummarizedExperiment-method se se,PlySummarizedExperiment-method se<- se<-,PlySummarizedExperiment-method |
| Plyxp Simple Example Summarized Experiment | se_simple |
| select assays, rowData, and colData names | select select.PlySummarizedExperiment |
| Summarize PlySummarizedExperiment | summarise summarise.PlySummarizedExperiment summarize summarize.PlySummarizedExperiment |
| Get observations of a vector | vctrs_slice vec_slice |
| Recycle a vector | vctrs-vec_recycle vec_recycle |
| replicate a vector | vctrs-vec_rep vec_rep vec_rep_each |
| Printing within tibble with S4 objects | plyxp-printing plyxp_pillar_format show_tidy use_show_default use_show_tidy vec_phantom |
| S7 classes for vctrs and S4 Vectors | class_DF class_s4_vctrs class_vctrs vectors |
