Package: plyxp 1.7.1
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_1.7.1.tar.gz
plyxp_1.7.1.zip(r-4.7)plyxp_1.7.1.zip(r-4.6)plyxp_1.7.1.zip(r-4.5)
plyxp_1.7.1.tgz(r-4.6-any)plyxp_1.7.1.tgz(r-4.5-any)
plyxp_1.7.1.tar.gz(r-4.7-any)plyxp_1.7.1.tar.gz(r-4.6-any)
plyxp_1.7.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
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/docs site:https://jtlandis.github.io
- se_simple - Plyxp Simple Example Summarized Experiment
On BioConductor:plyxp-1.7.1(bioc 3.24)plyxp-1.6.1(bioc 3.23)
annotationgenomeannotationtranscriptomics
Last updated from:b0150f6a82. Checks:1 WARNING, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 180 | ||
| linux-devel-x86_64 | OK | 343 | ||
| source / vignettes | OK | 269 | ||
| linux-release-x86_64 | OK | 320 | ||
| macos-release-arm64 | OK | 277 | ||
| macos-oldrel-arm64 | OK | 229 | ||
| windows-devel | OK | 275 | ||
| windows-release | OK | 224 | ||
| windows-oldrel | OK | 222 | ||
| wasm-release | OK | 161 |
Exports:.assays.assays_asis.cols.cols_asis.rows.rows_asisarrangeassayassay_ctxassay<-assaysassays<-class_DFclass_s4_vctrsclass_vctrscol_ctxcolDatacolData<-colnamescolsfiltergroup_bygroup_datagroup_splitgroup_varslist_unchopmetadatametadata<-mutatencolnew_plyxpnrowPlySummarizedExperimentplyxpplyxp_onplyxp_pillar_formatpullrow_ctxrowDatarowData<-rownamesrowssese<-selectshow_tidyslicesummarisesummarizeSummarizedExperimentungroupuse_show_defaultuse_show_tidyvec_chopvec_group_idvec_group_locvec_phantomvec_ptype_commonvec_ptype2vec_recyclevec_repvec_rep_eachvec_slice
Dependencies:abindBiobaseBiocGenericsclicpp11DelayedArraydplyrgenericsGenomicRangesglueIRangeslatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatspillarpkgconfigpurrrR6rlangS4ArraysS4VectorsS7SeqinfoSparseArraystringistringrSummarizedExperimenttibbletidyrtidyselectutf8vctrswithrXVector
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 |
| Split a PlySummarizedExperiment based on groups | group_split group_split.PlySummarizedExperiment |
| get PlySummarizedExperiment grouping Variables | group_vars group_vars.PlySummarizedExperiment |
| unchop a list of objects | list_unchop |
| Mutate a PlySummarizedExperiment object | mutate mutate.PlySummarizedExperiment |
| SummarizedExperiment Shell Object | new_plyxp PlySummarizedExperiment PlySummarizedExperiment-class |
| Modify SummarizedExperiment Object | plyxp plyxp_on |
| 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 colnames,PlySummarizedExperiment-method dimnames,PlySummarizedExperiment-method dimnames<-,PlySummarizedExperiment,list-method dimnames<-,PlySummarizedExperiment,NULL-method metadata,PlySummarizedExperiment-method metadata<-,PlySummarizedExperiment-method ncol,PlySummarizedExperiment-method nrow,PlySummarizedExperiment-method PlySummarizedExperiment-methods rowData,PlySummarizedExperiment-method rowData<-,PlySummarizedExperiment-method rownames,PlySummarizedExperiment-method se se,PlySummarizedExperiment-method se,SummarizedExperiment-method se<- se<-,PlySummarizedExperiment-method se<-,SummarizedExperiment-method |
| Plyxp Simple Example Summarized Experiment | se_simple |
| select assays, rowData, and colData names | select select.PlySummarizedExperiment |
| Slice a PlySummarizedExperiment | slice slice.PlySummarizedExperiment |
| Summarize PlySummarizedExperiment | summarise summarise.PlySummarizedExperiment summarize summarize.PlySummarizedExperiment |
| Get observations of a vector | vctrs_slice vec_slice |
| chop a vector | vctrs-vec_chop vec_chop |
| Recycle a vector | vctrs-vec_recycle vec_recycle |
| replicate a vector | vctrs-vec_rep vec_rep vec_rep_each |
| Create Group Indices | vec_group_id vec_group_loc |
| Printing within tibble with S4 objects | plyxp-printing plyxp_pillar_format show_tidy use_show_default use_show_tidy vec_phantom |
| find the common ptype | vec_ptype_common |
| Create a common prototype of two vectors | vec_ptype2 |
| S7 classes for vctrs and S4 Vectors | class_DF class_s4_vctrs class_vctrs vectors |
