| Type: | Package |
| Title: | From 'PLINK' to 'HIrisPlex' |
| Version: | 0.1.0 |
| Maintainer: | Andrea Giardina <andrea.giardina1@open.ac.uk> |
| Description: | Read 'PLINK' 1.9 binary datasets (BED/BIM/FAM) and generate the CSV files required by the Erasmus MC 'HIrisPlex' / 'HIrisPlex-S' webtool https://hirisplex.erasmusmc.nl/. It maps 'PLINK' alleles to the webtool's required 'rsID_Allele' columns (0/1/2/NA). No external tools (e.g., 'PLINK CLI') are required. |
| License: | MIT + file LICENSE |
| URL: | https://github.com/adhikari-statgen-lab/hirisplexr |
| BugReports: | https://github.com/adhikari-statgen-lab/hirisplexr/issues |
| Depends: | R (≥ 3.6) |
| Imports: | BEDMatrix, data.table, utils |
| Suggests: | testthat (≥ 3.0.0), knitr, rmarkdown |
| Config/testthat/edition: | 3 |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.3.2 |
| VignetteBuilder: | knitr |
| NeedsCompilation: | no |
| Packaged: | 2025-10-28 10:46:01 UTC; agiardina |
| Author: | Andrea Giardina 
[aut, cre] |
| Repository: | CRAN |
| Date/Publication: | 2025-10-31 18:20:17 UTC |
Write HIrisPlex / HIrisPlex-S CSV from a PLINK BED/BIM/FAM prefix
Description
Given a PLINK 1.9 binary dataset (prefix.bed/.bim/.fam), this function produces a CSV ready to upload to the HIrisPlex(-S) webtool.
Usage
write_hirisplex_csv(
prefix,
out,
panel = c("hirisplexs", "hirisplex", "irisplex"),
sample_id = c("IID", "FID_IID"),
allow_strand_flip = TRUE
)
Arguments
prefix |
Character. Path prefix to PLINK files, without extension. |
out |
Character. Output CSV path. |
panel |
Character. One of "hirisplexs" (default), "hirisplex", "irisplex".#' |
sample_id |
Character. How to form 'SampleID': "IID" or "FID_IID". Default is "IID". |
allow_strand_flip |
Logical. If TRUE, attempt to match the required allele by allowing strand complements. |
Details
Columns are 'SampleID' followed by one column per required SNP in the form
rsID_Allele (e.g., rs12203592_T). Each cell contains 0/1/2 (count of the
input allele) or NA when the SNP is missing. The column set and order are
defined by the selected panel (IrisPlex, HIrisPlex, HIrisPlex-S).
Allele counting is based on the PLINK .bim alleles. Genotype dosage is read
on demand from the .bed using BEDMatrix::BEDMatrix(), which encodes the
dosage of the first allele in the .bim file (A1). If the webtool's required
input allele equals A1, we use the dosage directly; if it equals A2, we use
(2 - dosage). If allow_strand_flip = TRUE, we also reconcile complements
(A<->T, C<->G) to account for strand orientation differences.
Value
(Invisibly) the output file path.
Examples
## Not run:
write_hirisplex_csv("/path/to/prefix", tempfile(fileext = ".csv"), panel = "hirisplexs")
## End(Not run)