Author: Brian Ward
Email: [email protected]
Github: etnite
License: MIT
This is a personal R package containing a collection of functions that I have written over time to help in my own research. I work in the field of wheat genetics, and therefore this package contains a mixture of functions relating to bioinformatics, genetics, and agronomic analyses. I have made it publicly available in case it might be of use to others, but please note that it lacks the polish of a CRAN-hosted package. Individual functions do have documentation, but there is no manual. Being that this is an R package, it is suited to moderately-sized genomic datasets. Those working with very large files will likely be better served using the usual purpose-built C/C++ or Java executables.
This package can be installed using the devtools package:
library(devtools)
install_github("etnite/bwardr")Or to install with vignettes:
library(devtools)
install_github("etnite/bwardr", build_vignettes = TRUE)Some demonstrations are forthcoming! However, the package includes (but is not limited to) the following functions:
- eigstrat() - an R port of the Eigenstrat algorithm for delineating population structure using principal component analysis of a SNP matrix
- stand_str() - a function for standardizing strings to a consistent format, to facilitate successful intersections of sets
- format_qtlmap_geno() - a function for converting VCF or PLINK binary PED (BED) files storing data on a biparental population into files suitable for input to R/qtl
- fdr_thresh() - finds an approximate p-value threshold corresponding to a specified false-discovery-rate threshold
- mc_train_val_multienv() - generate training/validation splits in multi-environment phenotypic datasets