PCBS - Principal Component BiSulfite

See our package site

Dependencies

PCBS is an R package with the following dependencies:

• tibble
• ggrepel
• ggplot2
• dplyr
• data.table

Data Setup

PCBS is a tool for analyzing WGBS datasets in a fast, flexible, and accurate fashion. PCBS is designed to pipe in Bismark-aligned WGBS data. The PCBS input file can be generated from bismark .cov files with the provided Bismark2Matrix.R script.

Usage: Rscript --vanilla Bismark2Matrix.R file_path file_tsv file_out

• file_path = /path/to/cov/files

• file_tsv = A three column, tab-separated file in this format:

  • filename | sample | group
  • sam1.cov | s1_trt | trt
  • sam2.cov | s2_ctl | ctl

• file_out = output file name

Important note: PCBS cannot handle CpGs that are NA an any sample, and these are removed by Bismark2Matrix.R. For this reason, PCBS is not recommended for sparse datasets.

Installation

install.packages("PCBS")

Usage

See our vignette