Import from .fam file or .ped file — plink_to_pedigree • Pedixplorer

Import a .fam or .ped file and return a Pedigree object

Usage

plink_to_pedigree(
  path,
  sep = "\t",
  quote = "'",
  header = FALSE,
  na_values = c("NA", "0")
)

Arguments

path: Path to the file
sep: Separator used in the file
quote: Quote used in the file
header: Boolean defining if the file has a header
na_values: A vector of strings that should be considered as NA

Value

A Pedigree object

Examples

write.table(
    data.frame(
        famid = c("1", "1", "1"),
        id = c("A", "B", "C"),
        dadid = c(0, 0, "A"),
        momid = c(0, 0, "B"),
        sex = c(1, 2, 1)
    ), file = "test.fam", sep = "\t", quote = FALSE,
    row.names = FALSE, col.names = FALSE
)
fam <- "test.fam"
pedi <- plink_to_pedigree(fam)