From PLINK to HIrisPlex

Overview

hirisplexr converts a PLINK 1.9 binary dataset (.bed/.bim/.fam) into the CSV format required by the HIrisPlex / HIrisPlex-S web application.

Output columns: SampleID + one rsID_Allele per SNP in the chosen panel.
Cell values: allele counts 0 / 1 / 2, or NA if missing.
Panels: IrisPlex (6 SNP), HIrisPlex (24 SNP), HIrisPlex-S (41 SNP).

Installation

# Install runtime deps
install.packages(c("BEDMatrix", "data.table"))
# Install this package from source tarball or local folder

Quick start

library(hirisplexr)
prefix <- "/path/to/your/prefix"  # without extension
outfile <-  tempfile(fileext = ".csv")
write_hirisplex_csv(prefix, panel = "hirisplexs", out = outfile)

How allele mapping works

BEDMatrix::BEDMatrix() yields the genotype dosage of A1 from the .bim file (values: 0/1/2).
For each required rsID_Allele:
- If the requested allele equals A1, we use the dosage directly.
- If it equals A2, we take 2 - dosage.
- If allow_strand_flip = TRUE, we also try the complement (A↔︎T, C↔︎G) to account for strand orientation; if no match is possible we write NA and emit a warning.

Palindromic SNPs

For A/T or C/G SNPs, complements equal the original bases. The function still uses the .bim allele pair (A1/A2) to determine the mapping. You should ensure that your BIM file uses a consistent reference across datasets.

Panels and order

The complete list of SNPs and their required input alleles is packaged in inst/extdata/hirisplex_panels.csv. The order of columns in the output CSV matches exactly the order used by the web application.

# Inspect packaged panel metadata
loader <- getFromNamespace(".load_hirisplex_panels", "hirisplexr")
head(loader())
#>        panel order        rsid input_allele   column_name
#> 42 hirisplex     1 rs312262906            A rs312262906_A
#> 43 hirisplex     2  rs11547464            A  rs11547464_A
#> 44 hirisplex     3    rs885479            T    rs885479_T
#> 45 hirisplex     4   rs1805008            T   rs1805008_T
#> 46 hirisplex     5   rs1805005            T   rs1805005_T
#> 47 hirisplex     6   rs1805006            A   rs1805006_A

Reproducibility tips

Keep .bed/.bim/.fam together under the same prefix.
If you update your PLINK files, regenerate the CSV to keep alleles consistent.
Track the package version used to produce the CSV in your analysis records.

Session info

sessionInfo()
#> R version 4.3.3 (2024-02-29)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: TUXEDO OS
#> 
#> Matrix products: default
#> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
#> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0
#> 
#> locale:
#>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
#>  [3] LC_TIME=it_IT.UTF-8        LC_COLLATE=C              
#>  [5] LC_MONETARY=it_IT.UTF-8    LC_MESSAGES=en_US.UTF-8   
#>  [7] LC_PAPER=it_IT.UTF-8       LC_NAME=C                 
#>  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
#> [11] LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C       
#> 
#> time zone: Europe/Rome
#> tzcode source: system (glibc)
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> loaded via a namespace (and not attached):
#>  [1] digest_0.6.34     R6_2.5.1          fastmap_1.1.1     xfun_0.41        
#>  [5] cachem_1.0.8      knitr_1.45        htmltools_0.5.7   rmarkdown_2.25   
#>  [9] lifecycle_1.0.4   cli_3.6.2         hirisplexr_0.1.0  sass_0.4.8       
#> [13] jquerylib_0.1.4   compiler_4.3.3    rstudioapi_0.15.0 tools_4.3.3      
#> [17] evaluate_0.23     bslib_0.6.1       yaml_2.3.8        rlang_1.1.3      
#> [21] jsonlite_1.8.8