| Title: | From PLINK to HIrisPlex |
|---|---|
| Description: | Read PLINK 1.9 binary datasets (BED/BIM/FAM) and generate the CSV files required by the Erasmus MC HIrisPlex / HIrisPlex-S webtool. 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. |
| Authors: | Andrea Giardina [aut, cre] |
| Maintainer: | Andrea Giardina <[email protected]> |
| License: | MIT + file LICENSE |
| Version: | 0.1.0 |
| Built: | 2026-06-07 06:36:27 UTC |
| Source: | https://github.com/adhikari-statgen-lab/hirisplexr |
Given a PLINK 1.9 binary dataset (prefix.bed/.bim/.fam), this function produces a CSV ready to upload to the HIrisPlex(-S) webtool.
write_hirisplex_csv( prefix, panel = c("hirisplexs", "hirisplex", "irisplex"), out = NULL, sample_id = c("IID", "FID_IID"), allow_strand_flip = TRUE )write_hirisplex_csv( prefix, panel = c("hirisplexs", "hirisplex", "irisplex"), out = NULL, sample_id = c("IID", "FID_IID"), allow_strand_flip = TRUE )
prefix |
Character. Path prefix to PLINK files, without extension. |
panel |
Character. One of "hirisplexs" (default), "hirisplex", "irisplex". |
out |
Character. Output CSV path. Defaults to |
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. |
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.
(Invisibly) the output file path.
## Not run: write_hirisplex_csv("/path/to/prefix", panel = "hirisplexs") ## End(Not run)## Not run: write_hirisplex_csv("/path/to/prefix", panel = "hirisplexs") ## End(Not run)