rfPIPeak

An R package for peak calling Chem-seq data from pyrrole-imidazole (PI) polyamide affinity-enriched whole genome sequencing data using random forests.

June 30, 2020: initial package structure uploaded (version 0.0.1000)
August 25, 2020: updated Perl internals

Note: a decision was made to merge rfPIPeak with PPSI, the previous Chem-seq peak assignment tool. The new tool will use R as the primary interface, and thus is currently undergoing a major rewrite to combine the two. As such, the codes included herein are to be continually updated and not considered fully functional until version 0.1.0000

System Requirements

1. A macOS/Linux environment (WSL may also be compatible)
2. Perl version 5.16 or above
3. R version >3.3 (version 3.4.1 or above recommended)
4. gcc and GNU Fortran (version 4.8 or above should work)
5. CRED
6. htslib

Perl Dependencies

• PerlIO::gzip
• Parallel::ForkManager
• Inline::C
• File::Type
• Math::CDF
• Statistics::TTest

R Dependencies

• ranger
• data.table
• compiler
• stats
• parallel
• ggplot2

Installation

Note: from this point on all code blocks are R codes

library("devtools") # install.packages("devtools")
devtools::install_github("jlincbio/rfpipeak")

After installation of the package, rfPIPeak.setup() needs to be executed to properly configure some of the non-R components. At that time there will also be a check on whether your C compiler supports OpenMP (highly recommended as part of the package uses data.table that can benefit from it), and if htslib is also installed. You also need to set an addition environmental variable named HTSLIB that points to the location of htslib.

Miscellaneous

The current version also contains a number of convenience functions that will be removed upon the upload of the final stable version.

Citations

J. Lin, T. Kuo, P. Horton, H. Nagase, "CRED: a rapid peak caller for Chem-seq data." J. Open Source Softw. 4(37): 1423, 2019. DOI: 10.21105/joss.01423

J. Lin, K. Hiraoka, T. Watanabe, T. Kuo et al, "Identification of Binding Targets of a Pyrrole-Imidazole Polyamide KR12 in the LS180 Colorectal Cancer Genome." PLoS ONE 11(10): e0165581, 2016. DOI: 10.1371/journal.pone.0165581

rfPIPeak also includes tidbits of code from various sources, including but not limited to:

• diffReps: L. Shen et al, PLoS ONE 8(6): e65598, 2013
• uthash: T. Hanson (https://github.com/troydhanson/uthash
• NuPoP: L. Xi et al, BMC Bioinformatics 11: 346, 2010

(List will be updated over time)

In R: citation("rfPIPeak")