pedtricks (version 0.4.2)

convert_ped: Converts a pedigree with individuals specified as factors to a numeric pedigree

Description

Some internal pedtricks modules require that pedigrees be specified only by numerical values, or including numerical values for missing data. This function provides the conversion to numeric but also back to factors if needed

Usage

convert_ped(type = "numeric", id, sire, dam, missingVal = NA, key = NULL)

Value

numericPedigree

The factor pedigree in numeric form

idKey

A key to facilitate conversion back to the original identifiers

Arguments

type

define how to convert the pedigree so "numeric" or "factor"

id

Individual identifiers - pass using as.character()

sire

Sire codes - pass using as.character()

dam

Dam codes - pass using as.character()

missingVal

the indicator that should be substituted for missing values

key

A dataframe, as produced by convert_ped, specifying factor codes for numeric values in id, sire, and dam

Examples

pedigree <- as.data.frame(matrix(c(
  "m1",   NA,     NA,
  "m2",   NA,     NA,
  "m3",   NA,     NA,
  "d4",   NA,     NA,
  "d5",   NA,     NA,
  "o6",   "m1",   "d4",
  "o7",   "m1",   "d4",
  "o8",   "m1",   "d4",
  "o9",   "m1",   "d4",
  "o10",  "m2",   "d5",
  "o11",  "m2",   "d5",
  "o12",  "m2",   "d5",
  "o13",  "m2",   "d5",
  "o14",  "m3",   "d5",
  "o15",  "m3",   "d5",
  "o16",  "m3",   "d5",
  "o17",  "m3",   "d5"
), 17, 3, byrow = TRUE))
names(pedigree) <- c("id", "dam", "sire")
for (x in 1:3) pedigree[, x] <- as.factor(pedigree[, x])

## make the test pedigree numeric with NAs denoted by -1
convert_ped(
  type = "numeric",
  id = as.character(pedigree[, 1]),
  dam = as.character(pedigree[, 2]),
  sire = as.character(pedigree[, 3]),
  missingVal = -1
)