Read a twin/zygosity relations table from a file — readTwinRelations • nprcgenekeepr

Reads a user-supplied twin-relations sidecar table into a data frame for checkTwinRelations. The expected form is id1, id2, code, with a header row (see checkTwinRelations for the accepted code values). Excel (.xls/.xlsx) and delimited text (.csv/ .txt) files are both accepted, mirroring readKinshipOverrides – the closest existing precedent for a validated, pairwise sidecar upload (issue #137 D1/D5, docs/planning/issue137-twin-zygosity-pedigree-diagram-plan.md).

Usage

readTwinRelations(fileName, sep = ",")

Arguments

fileName: character vector of length one; path to the twin -relations file (typically the temporary datapath from a Shiny file upload).
sep: column separator for delimited text files (default ","). Ignored for Excel files.

Value

A data frame of the rows read from fileName (typically with columns id1, id2, and code). Validate it with checkTwinRelations before use.

Details

This reader does not validate structure or domain – that is checkTwinRelations's job.

Examples

ped <- data.frame(
  id = c("F1", "F2", "S1", "S2"),
  sire = c(NA, NA, "F1", "F1"),
  dam = c(NA, NA, "F2", "F2"),
  sex = c("M", "F", "F", "F"),
  stringsAsFactors = FALSE
)
csvFile <- tempfile(fileext = ".csv")
writeLines(c("id1,id2,code", "S1,S2,MZ twin"), csvFile)
twinRelations <- readTwinRelations(fileName = csvFile)
twinRelations <- checkTwinRelations(ped, twinRelations)
twinRelations
#>   id1 id2    code
#> 1  S1  S2 MZ twin
unlink(csvFile)