convert_ped {pedtricks} | R Documentation |
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
convert_ped(type = "numeric", id, sire, dam, missingVal = NA, key = NULL)
type |
define how to convert the pedigree so "numeric" or "factor" |
id |
Individual identifiers - pass using |
sire |
Sire codes - pass |
dam |
Dam codes - pass |
missingVal |
the indicator that should be substituted for missing values |
key |
A dataframe, as produced by |
numericPedigree |
The factor pedigree in numeric form |
idKey |
A key to facilitate conversion back to the original identifiers |
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
)