convert_ped {pedtricks} | R Documentation |
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)
Arguments
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 |
Value
numericPedigree |
The factor pedigree in numeric form |
idKey |
A key to facilitate conversion back to the original identifiers |
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
)
[Package pedtricks version 0.4.2 Index]