Package: PCBS 0.1.1

PCBS: Principal Component BiSulfite

A system for fast, accurate, and flexible whole genome bisulfite sequencing (WGBS) data analysis of two-condition comparisons. Principal Component BiSulfite, 'PCBS', assigns methylated loci eigenvector values from the treatment-delineating principal component in lieu of running millions of pairwise statistical tests, which dramatically increases analysis flexibility and reduces computational requirements. Methods: <https://katlande.github.io/PCBS/articles/Differential_Methylation.html>.

Authors:Kathryn Lande [aut, cre, cph]

PCBS_0.1.1.tar.gz
PCBS_0.1.1.zip(r-4.7)PCBS_0.1.1.zip(r-4.6)PCBS_0.1.1.zip(r-4.5)
PCBS_0.1.1.tgz(r-4.6-any)PCBS_0.1.1.tgz(r-4.5-any)
PCBS_0.1.1.tar.gz(r-4.7-any)PCBS_0.1.1.tar.gz(r-4.6-any)
PCBS_0.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
PCBS/json (API)

# Install 'PCBS' in R:

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

Bug tracker:https://github.com/katlande/pcbs/issues

Datasets:

eigen - Simulated WGBS data for PCBS vignettes

On CRAN:

2.70 score 1 stars 148 downloads 24 exports 28 dependencies

Last updated from:c26e14189d. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	140
source / vignettes	OK	153
linux-release-x86_64	OK	170
macos-release-arm64	OK	175
macos-oldrel-arm64	OK	189
windows-devel	OK	133
windows-release	OK	95
windows-oldrel	OK	97
wasm-release	OK	97

Exports:addRanks CheckOvercompression checkRank chromDict chromDictMeth DefineBestPC get_all_DMRs Get_Novel_DMRs getPCRanks getRegionScores lin lmIntx MethyDiff_Set MethylDiff methylDiff_metagene multiple_metagenes Ol_Reliable oneSeed plot_metagene rankDist score_metagene se tilt trimDMR

Dependencies:cli cpp11 data.table dplyr farver generics ggplot2 ggrepel glue gtable isoband labeling lifecycle magrittr pillar pkgconfig R6 RColorBrewer Rcpp rlang S7 scales tibble tidyselect utf8 vctrs viridisLite withr

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Add ranks to eigenvector scores.	addRanks
Check if DMR calling seed number is ovcompressed.	CheckOvercompression
Check rank cut-off values manually.	checkRank
Convert a rank object into a chromDict.	chromDict
Create a chromDict of percent methylation difference at all sites.	chromDictMeth
Identify your best principle component.	DefineBestPC
Simulated WGBS data for PCBS vignettes	eigen
Nested DMR calling function within Get_Novel_DMRs()	get_all_DMRs
Call DMRs from WGBS data.	Get_Novel_DMRs
Get CpG eigenvector scores from a principle component.	getPCRanks
Calculated methylation significance in a set of regions.	getRegionScores
Find y value of linear regression given x.	lin
PC-Intersect nested function.	lmIntx
Add a mean methylation column to a data.frame of regions.	MethyDiff_Set
Get the mean methylation difference across a specified region.	MethylDiff
Make a metagene from mean percent methylation differences.	methylDiff_metagene
Plot multiple metagene data objects on a single plot.	multiple_metagenes
PCBS ggplot theme.	Ol_Reliable
Nested DMR calling function within within get_all_DMRs(), Get_Novel_DMRs()	oneSeed
Generate a metagene plot from raw metagene data.	plot_metagene
Identify the best rank cut-off for significant CpGs.	rankDist
Make a metagene from PC Scores.	score_metagene
Standard error of a vector.	se
Component of PCBS ggplot theme.	tilt
Nested DMR calling function within within Get_Novel_DMRs()	trimDMR