Package: plyxp 0.99.24

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:Justin Landis [aut, cre], Michael Love [aut]

plyxp_0.99.24.tar.gz
plyxp_0.99.24.zip(r-4.5)plyxp_0.99.24.zip(r-4.4)
plyxp_0.99.24.tgz(r-4.4-any)
plyxp_0.99.24.tar.gz(r-4.5-noble)plyxp_0.99.24.tar.gz(r-4.4-noble)
plyxp_0.99.24.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'))

Peer review:

Bug tracker:https://github.com/jtlandis/plyxp/issues

Datasets:
  • se_simple - Plyxp Simple Example Summarized Experiment

On BioConductor:plyxp-0.99.23(bioc 3.20)

annotationgenomeannotationtranscriptomics

4.90 score 2 scripts 50 exports 49 dependencies

Last updated 1 days agofrom:b6287e35d6. Checks:OK: 5. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 29 2024
R-4.5-winOKOct 29 2024
R-4.5-linuxOKOct 29 2024
R-4.4-winOKOct 29 2024
R-4.4-macOKOct 29 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

plyxp Usage Guide

Rendered fromplyxp.Rmdusingknitr::rmarkdownon Oct 29 2024.

Last update: 2024-10-21
Started: 2024-10-16

Readme and manuals

Help Manual

Help pageTopics
arrange rows or columns of PlySummarizedExperimentarrange arrange.PlySummarizedExperiment
create data.frameas.data.frame as.data.frame.PlySummarizedExperiment
contextual plyxp pronouns.assays .assays_asis .cols .cols_asis .rows .rows_asis dot-pronouns
filter PlySummarizedExperimentfilter filter.PlySummarizedExperiment
apply groups to PlySummarizedExperimentgroup_by group_by.PlySummarizedExperiment ungroup.PlySummarizedExperiment
get grouping datagroup_data group_data.PlySummarizedExperiment ungroup
get PlySummarizedExperiment grouping Variablesgroup_vars group_vars.PlySummarizedExperiment
Mutate a PlySummarizedExperiment objectmutate mutate.PlySummarizedExperiment
SummarizedExperiment Shell Objectnew_plyxp PlySummarizedExperiment PlySummarizedExperiment-class
Modify SummarizedExperiment Objectplyxp
plyxp contextsassay_ctx cols col_ctx plyxp-context rows row_ctx
extract data from objectpull pull.PlySummarizedExperiment
PlySummarizedExperiment Methodsassay,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 Experimentse_simple
select assays, rowData, and colData namesselect select.PlySummarizedExperiment
Summarize PlySummarizedExperimentsummarise summarise.PlySummarizedExperiment summarize summarize.PlySummarizedExperiment
Get observations of a vectorvctrs_slice vec_slice
Recycle a vectorvctrs-vec_recycle vec_recycle
replicate a vectorvctrs-vec_rep vec_rep vec_rep_each
Printing within tibble with S4 objectsplyxp-printing plyxp_pillar_format show_tidy use_show_default use_show_tidy vec_phantom
S7 classes for vctrs and S4 Vectorsclass_DF class_s4_vctrs class_vctrs vectors