Check a locus-metadata sidecar table and classify per-locus coverage

Validates the structure of a locus-metadata sidecar table (locus, chrom, pos, and optionally cM) – the schema introduced by issue #152's own design decision and reused verbatim by issue #153 – and classifies each locus into one of three coverage tiers, following a PLINK-style three-state coverage model: "full" (both chrom and pos present; cM is optional even within "full"), "partial" (exactly one of chrom/pos present), or "none" (neither present).

Usage

checkLocusMetadata(locusMetadata)

Arguments

locusMetadata: dataframe with locus metadata: three or four columns, locus, chrom, pos, and optionally cM (one row per locus).

Value

The locus-metadata dataframe, checked to ensure the column count, first-column identity, and row uniqueness are all valid, with a new coverage column appended ("full"/"partial"/ "none"). The returned dataframe has locus and chrom coerced to character.

Details

A locus-metadata table has one row per locus (not per individual x locus, unlike checkMarkerGenotypeFile's genotype table). Real curated marker panels typically supply little to no locus-order metadata – this function reports coverage explicitly per locus rather than requiring complete metadata before any downstream use.

References

Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D., Maller, J., Sklar, P., de Bakker, P. I. W., Daly, M. J., & Sham, P. C. (2007). PLINK: a tool set for whole-genome association and population-based linkage analyses. American Journal of Human Genetics, 81(3), 559-575. doi:10.1086/519795

Examples

library(nprcgenekeepr)
locusMetadata <- data.frame(
  locus = c("L1", "L2", "L3"),
  chrom = c("1", "1", NA),
  pos = c(1000000, NA, NA),
  stringsAsFactors = FALSE
)
checkLocusMetadata(locusMetadata)
#>   locus chrom   pos coverage
#> 1    L1     1 1e+06     full
#> 2    L2     1    NA  partial
#> 3    L3  <NA>    NA     none