snpR

snpR is an R package for analyzing call Single Nucleotide Polymorphism (SNP) genotypes containing most basic stats including pairwise LD, gaussian sliding window analysis tools, plotting options, clustering analysis, colony interface, Ne estimation, formatting, filtering, and more!

Installation

snpR can be installed from GitHub:

# install.packages("remotes")
remotes::install_github("hemstrow/snpR")

To install the vignettes as well (recommended for new users), instead use:

remotes::install_github("hemstrow/snpR", build_vignettes = T) # linux
remotes::install_github("hemstrow/snpR", ref = "dev", build_vignettes = T, build_opts = c("--no-resave-data", "--no-manual")) # windows

The dev version can be installed from GitHub as well:

# install.packages("remotes")
remotes::install_github("hemstrow/snpR", ref = "dev")

A CRAN version should be available soon.

Example

snpR is focused on ease-of-use. Primarily, it achieves this via the use of , which describe sample or SNP metadata. snpR is built to automatically split up analysis by facet. For example, calculating genetic diversity (pi) for each population or family, or for each population/family combination is easy!

library(snpR)
#> Loading required package: data.table
#> Loading required package: doParallel
#> Loading required package: foreach
#> Loading required package: iterators
#> Loading required package: parallel
## basic example code

x <- calc_pi(stickSNPs, facets = c("pop")) # split by pop (stickSNPs is an example dataset included in snpR)
x <- calc_pi(x, facets = c("fam")) # split by family
x <- calc_pi(x, facets = c("pop.fam")) # split by combinations of family and pop

snpR also facilitates ease-of-use by being . As above, new analyses are added to an existing object. Results can be fetched using the get.snpR.stats handler.

head(get.snpR.stats(x))
#>   facet subfacet  snp    group position .snp.id major minor maj.count min.count
#> 1 .base    .base 4529   groupV    42825       1     C     T       791        23
#> 2 .base    .base 6829 groupXIX    67921       2     C     G       515       213
#> 3 .base    .base 1674  groupIX   100382       3     G     A       739        53
#> 4 .base    .base 9790   groupX   101821       4     C     T       752        46
#> 5 .base    .base 5803 groupXIV   175941       5     G     A       719        53
#> 6 .base    .base 2366   groupI   182629       6     C     T       642        22
#>          maf pi
#> 1 0.02825553 NA
#> 2 0.29258242 NA
#> 3 0.06691919 NA
#> 4 0.05764411 NA
#> 5 0.06865285 NA
#> 6 0.03313253 NA

For a full introduction, check the snpR_introduction vignette.

# remotes::install_github("hemstrow/snpR", ref = "dev", build_vignettes = T, build_opts = c("--no-resave-data", "--no-manual"))

vignette("snpR_introduction")
#> Warning: vignette 'snpR_introduction' not found