De-identify a computeGenomicROH() result table

Remaps the id column of a computeGenomicROH result table through the same alias vector obfuscatePed(..., map = TRUE) already returns, mirroring obfuscateTwinRelations's and obfuscateGenotypeMatrix's pattern (issue #152 Slice 5, design decision D7: "any sequence-derived export... routes through a new de-identification primitive"). computeGenomicROH's output is a plain per-individual data.frame keyed by a single id column – a different shape from every prior obfuscate*() sibling, so none of them fit directly.

Usage

obfuscateGenomicROH(rohTable, map)

Arguments

rohTable

data.frame as returned by computeGenomicROH: at least an id column.

map

named character vector of aliases, keyed by the original id – the map element of obfuscatePed(..., map = TRUE)'s return value.

Value

rohTable with id replaced by its alias; every other column (nSegments, totalRohLength, fRoh) is unchanged.

Details

A row whose id is absent from map stop()s rather than silently dropping or leaking the real id.

See also

Other obfuscation: mapIdsToObfuscated(), obfuscateDate(), obfuscateGenotypeMatrix(), obfuscateId(), obfuscateLdBlocks(), obfuscatePed(), obfuscateTwinRelations()

Examples

library(nprcgenekeepr)
ped <- data.frame(
  id = c("A01", "A02"),
  sire = c(NA, NA),
  dam = c(NA, NA),
  sex = c("M", "F"),
  stringsAsFactors = FALSE
)
rohTable <- data.frame(
  id = c("A01", "A02"), nSegments = c(1L, 0L),
  totalRohLength = c(1000000, 0), fRoh = c(0.1, 0),
  stringsAsFactors = FALSE
)
obfuscated <- obfuscatePed(ped, map = TRUE)
obfuscateGenomicROH(rohTable, obfuscated$map)
#>       id nSegments totalRohLength fRoh
#> 1 QX9SRG         1          1e+06  0.1
#> 2 1QSHIV         0          0e+00  0.0