Read a kinship overrides table from a file

Reads an outside-information kinship override table from a user-supplied file into a data frame for checkKinshipOverrides and reportGV. The expected long form is the output of kinMatrix2LongForm: columns id1, id2, and kinship, with a header row, so a user can export the current matrix, edit a few rows, and feed it back. Excel (.xls/.xlsx) and delimited text (.csv/.txt) files are both accepted, mirroring getGenotypes. Excel files are read with every column as text and then the kinship column is converted to numbers, so an Excel file and a delimited text file of the same table give the same result. If any value in that column is not a number, the column is left as text and checkKinshipOverrides stops, naming it.

Usage

readKinshipOverrides(fileName, sep = ",")

Arguments

fileName

character vector of length one; path to the override 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 kinship). Validate it with checkKinshipOverrides before use.

Details

This reader does not validate structure or domain – that is checkKinshipOverrides's job. kinship is the kinship coefficient f, not the coefficient of relatedness r (= 2f for non-inbred animals).

Examples

csvFile <- tempfile(fileext = ".csv")
writeLines(c("id1,id2,kinship", "A1,A2,0.25", "A3,A4,0.125"), csvFile)
overrides <- readKinshipOverrides(fileName = csvFile)
overrides <- checkKinshipOverrides(overrides)
overrides
#>   id1 id2 kinship
#> 1  A1  A2   0.250
#> 2  A3  A4   0.125
unlink(csvFile)