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

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✨
DESCRIPTION |NEWS
card.svg |card.png
plyxp/json (API)

# 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

Datasets:

se_simple - Plyxp Simple Example Summarized Experiment

On BioConductor:plyxp-1.7.1(bioc 3.24)plyxp-1.6.1(bioc 3.23)

annotation genomeannotation transcriptomics

7.20 score 9 stars 2 packages 21 scripts 63 exports 37 dependencies

Last updated from:b0150f6a82. Checks:1 WARNING, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	195
linux-devel-x86_64	OK	353
source / vignettes	OK	261
linux-release-x86_64	OK	358
macos-release-arm64	OK	211
macos-oldrel-arm64	OK	160
windows-devel	OK	251
windows-release	OK	218
windows-oldrel	OK	205
wasm-release	OK	177

Exports:.assays .assays_asis .cols .cols_asis .rows .rows_asis arrange assay assay_ctx assay<-assays assays<-class_DF class_s4_vctrs class_vctrs col_ctx colData colData<-colnames cols filter group_by group_data group_split group_vars list_unchop metadata metadata<-mutate ncol new_plyxp nrow PlySummarizedExperiment plyxp plyxp_on plyxp_pillar_format pull row_ctx rowData rowData<-rownames rows se se<-select show_tidy slice summarise summarize SummarizedExperiment ungroup use_show_default use_show_tidy vec_chop vec_group_id vec_group_loc vec_phantom vec_ptype_common vec_ptype2 vec_recycle vec_rep vec_rep_each vec_slice

Dependencies:abind Biobase BiocGenerics cli cpp11 DelayedArray dplyr generics GenomicRanges glue IRanges lattice lifecycle magrittr Matrix MatrixGenerics matrixStats pillar pkgconfig purrr R6 rlang S4Arrays S4Vectors S7 Seqinfo SparseArray stringi stringr SummarizedExperiment tibble tidyr tidyselect utf8 vctrs withr XVector

plyxp Usage Guide

Rendered fromplyxp.Rmdusingknitr::rmarkdown

Last update: 2026-02-15
Started: 2024-10-16

Citation

Development and contributors

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