Converts a pedigree with individuals specified as factors to a numeric pedigree
Source:R/convert_ped.R
convert_ped.RdSome 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
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
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
)
#> $numericPedigree
#> id sire dam
#> 1 3 -1 -1
#> 2 4 -1 -1
#> 3 5 -1 -1
#> 4 1 -1 -1
#> 5 2 -1 -1
#> 6 14 1 3
#> 7 15 1 3
#> 8 16 1 3
#> 9 17 1 3
#> 10 6 2 4
#> 11 7 2 4
#> 12 8 2 4
#> 13 9 2 4
#> 14 10 2 5
#> 15 11 2 5
#> 16 12 2 5
#> 17 13 2 5
#>
#> $idKey
#> pn pf
#> 1 3 m1
#> 2 4 m2
#> 3 5 m3
#> 4 1 d4
#> 5 2 d5
#> 6 14 o6
#> 7 15 o7
#> 8 16 o8
#> 9 17 o9
#> 10 6 o10
#> 11 7 o11
#> 12 8 o12
#> 13 9 o13
#> 14 10 o14
#> 15 11 o15
#> 16 12 o16
#> 17 13 o17
#> 18 -1 <NA>
#>