See our github repo.
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 or Bismark2Matrix.py scripts. The python and R versions of these scripts create the same output file, and have more or less identical usage. 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
- file_path = /path/to/cov/files
- file_out = output file name
- file_tsv = A three column, tab-separated file in this format:
| filename | sample | group |
|---|---|---|
| sam1.cov | s1_trt | trt |
| sam2.cov | s2_ctl | ctl |
Usage
See our vignette