We present an R package, named pasaR, usable in the later stages of an pangenomic analysis, i.e. after the construction of the gene families for a given set of genomes, based on information of the full complement of gene families. A complete methodology is proposed, suitable for sets of genomes of varying complexity, optimizing and enriching an assortment of existing measures from micropan, the only R package currently available on CRAN for such studies. This is an on-going project so better documentantion, a more extensive vignette and additional functions will be added. However the package is fully functional.
If package devtools is present, simply run:
library(devtools)
install_github("ampatzia/PasaR")Currently there are available two vignettes for the package, both precompiled in pdf:
- Small case study and example of usage in a pangenome of 81 bacterial strains. .
- Benchmark comparison to package micropan .
Mpatziakas A, Psomopoulos FE, Moysiadis T and Sgardelis S. Computing pangenome statistics in R. F1000Research 2017, 6(ISCB Comm J):1529 (poster) (doi: 10.7490/f1000research.1114765.1)
Any questions should be directed to ampatziakas at gmail.com