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hirisplexr

Build HIrisPlex / HIrisPlex-S CSV files directly from PLINK 1.9 BED/BIM/FAM.

Installation (from source)

# in R
install.packages("BEDMatrix")
install.packages("data.table")

# build & install this package (using R CMD build/check/INSTALL or devtools)

Usage

library(hirisplexr)

# Example prefix chosen for documentation purposes
# (provide your own PLINK files at this path)
prefix <- "inst/extdata/testprefix"

write_hirisplex_csv(prefix, panel = "hirisplexs", out = "hirisplexs.csv")

How it works

• Genotypes are read on-demand from .bed using [BEDMatrix], which returns dosages of A1 (first allele in .bim).
• The HIrisPlex(-S) webtool requires a count (0/1/2) of a specific input allele for each SNP. We map A1/A2 to that input allele; for strand issues we can also consider complements.

Panels

Panel definitions (rsID and required input allele, in the precise order expected by the webtool) are packaged in inst/extdata/hirisplex_panels.csv. They are sourced from the official webtool and manual (see citations below).

Citations

• HIrisPlex-S webtool: https://hirisplex.erasmusmc.nl/ (columns and upload format)
• HIrisPlex-S user manual (2018), Erasmus MC (instructions and caveats)
  • Notes include: count of 0/1/2 per SNP; use NA if missing; rs6119471 may require strand conversion from NCBI forward.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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