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). A value counts as present when it is not NA, so an empty-string chrom counts as 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, and its column names forced to locus, chrom, pos (and cM when there are four columns) whatever the input names were.

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