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PCBS (version 0.1.1)

Principal Component BiSulfite

Description

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: .

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Install

install.packages('PCBS')

Monthly Downloads

240

Version

0.1.1

License

GPL-3

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Repository

https://github.com/katlande/PCBS

Maintainer

Kathryn Lande

Last Published

August 27th, 2024

Functions in PCBS (0.1.1)

Call DMRs from WGBS data.

PCBS ggplot theme.

Add a mean methylation column to a data.frame of regions.

methylDiff_metagene

Make a metagene from mean percent methylation differences.

Make a metagene from PC Scores.

multiple_metagenes

Plot multiple metagene data objects on a single plot.

Nested DMR calling function within Get_Novel_DMRs()

CheckOvercompression

Check if DMR calling seed number is ovcompressed.

Convert a rank object into a chromDict.

Generate a metagene plot from raw metagene data.

Create a chromDict of percent methylation difference at all sites.

Identify your best principle component.

Add ranks to eigenvector scores.

Simulated WGBS data for PCBS vignettes

Get CpG eigenvector scores from a principle component.

Check rank cut-off values manually.

Find y value of linear regression given x.

getRegionScores

Calculated methylation significance in a set of regions.

PC-Intersect nested function.

Nested DMR calling function within within Get_Novel_DMRs()

Identify the best rank cut-off for significant CpGs.

Nested DMR calling function within within get_all_DMRs(), Get_Novel_DMRs()

Standard error of a vector.

Component of PCBS ggplot theme.

Get the mean methylation difference across a specified region.