Package: planet 1.21.0

Victor Yuan

planet: Placental DNA methylation analysis tools

This package contains R functions to predict biological variables to from placnetal DNA methylation data generated from infinium arrays. This includes inferring ethnicity/ancestry, gestational age, and cell composition from placental DNA methylation array (450k/850k) data.

Authors:Victor Yuan [aut, cre], Wendy P. Robinson [aut, ctb], Icíar Fernández-Boyano [aut, ctb]

planet_1.21.0.tar.gz
planet_1.21.0.zip(r-4.7)planet_1.21.0.zip(r-4.6)planet_1.21.0.zip(r-4.5)
planet_1.21.0.tgz(r-4.6-any)planet_1.21.0.tgz(r-4.5-any)
planet_1.21.0.tar.gz(r-4.7-any)planet_1.21.0.tar.gz(r-4.6-any)
planet_1.21.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
planet/json (API)

# Install 'planet' in R:

install.packages('planet', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/wvictor14/planet/issues

Pkgdown/docs site:https://victoryuan.com

Datasets:

ageCpGs - Placental gestational age CpGs
ethnicityCpGs - CpGs to predict ethnicity
plBetas - Example placental DNA methylation data
plCellCpGsFirst - First trimester placental cell type coefficients
plCellCpGsThird - Third trimester placental cell type coefficients
plColors - A color palette for placental cell types
plPhenoData - Sample information accompanying 'pl_betas'

On BioConductor:planet-1.21.0(bioc 3.24)planet-1.20.0(bioc 3.23)

software differentialmethylation epigenetics microarray methylationarray dnamethylation cpgisland ancestry dna-methylation-data genetics inference machine-learning placenta

6.09 score 4 stars 1 packages 34 scripts 1 mentions 4 exports 15 dependencies

Last updated from:8086bc5eb5. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	187
linux-devel-x86_64	NOTE	472
source / vignettes	OK	309
linux-release-x86_64	NOTE	219
macos-release-arm64	NOTE	109
macos-oldrel-arm64	NOTE	128
windows-devel	NOTE	139
windows-release	NOTE	129
windows-oldrel	NOTE	788
wasm-release	OK	198

Exports:%>%predictAge predictEthnicity predictPreeclampsia

Dependencies:cli dplyr generics glue lifecycle magrittr pillar pkgconfig R6 rlang tibble tidyselect utf8 vctrs withr

planet

Rendered fromplanet.Rmdusingknitr::rmarkdown

Last update: 2025-02-01
Started: 2021-03-10

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Placental gestational age CpGs	ageCpGs
CpGs to predict ethnicity	ethnicityCpGs
Example placental DNA methylation data	plBetas
First trimester placental cell type coefficients	plCellCpGsFirst
Third trimester placental cell type coefficients	plCellCpGsThird
A color palette for placental cell types	plColors
Sample information accompanying 'pl_betas'	plPhenoData
predict mixxo from	predict predict.mixo_pls predict.mixo_spls
Predicts gestational age using placental DNA methylation microarray data	predictAge
Predicts ethnicity using placental DNA methylation microarray data	predictEthnicity
predictPreeclampsia	predictPreeclampsia