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PCBS - Principal Component BiSulfite

See our package site

Dependencies

PCBS is an R package with the following dependencies:

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

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

Installation

install.packages("PCBS")


Usage

See our vignette