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 scripts (we offer scripts for R and Python with identical usage and output). We recommend using the Python version of this script as it is faster.

Python Usage: python Bismark2Matrix.py -p file_path -i file_tsv -o file_out

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

For both Python and R, the inputs are identical:

• 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. For this reason, PCBS is not recommended for sparse datasets.

Installation

Install the published version

install.packages("PCBS")

Install the latest updates

remotes::install_github("katlande/PCBS")

Usage

See our vignette