rPHG2
is a system to interact with and retrieve information from version 2 of the Practical Haplotype Graph (PHGv2) - a general, graph-based, computational framework for genotype inference. This is accomplished by leveraging the Breeding and PHG APIs.
Installation
You can install the development version of rphg2 from GitHub with:
# install.packages("pak")
pak::pak("maize-genetics/rPHG2")
Usage
# Initialize with PHGv2 JARs
initPhg("my/phg/jar/path")
# Create a connection
locCon <- list.files("my/hvcf/dir") |>
PHGLocalCon()
# Build a graph
graph <- locCon |> buildHaplotypeGraph()
# Read data into R
phgDs <- graph |> readPhgDataSet()
# Identify areas of interest
gr <- GRanges(
seqnames = c("1", "2"),
ranges = IRanges(
c(100, 800),
c(400, 900)
)
)
phgDs |>
filterSamples(c("B73", "Ky21", "Mo17")) |>
filterRefRanges(gr)
Lifecycle
rPHG2
is a relatively new R package and may be subject to changes in workflow and function definitions. If you would like to see anything added or run into problems, please feel free to contact the team using the issues page.