sample.ped.geno {famSKATRC} | R Documentation |
Sample Pedigree Genotype Data
Description
A sample pedigree file with SNP data, already processed by the process_data() function. The raw data is also included in the package.
Usage
data("sample.ped.geno")
Format
A data frame with 20 observations on the following 36 variables.
FID
a numeric vector
IID
a character vector
FA
a character vector
MO
a character vector
SEX
a numeric vector
Phenotype
a numeric vector
rs1
a numeric vector
rs2
a numeric vector
rs3
a numeric vector
rs4
a numeric vector
rs5
a numeric vector
rs6
a numeric vector
rs7
a numeric vector
rs8
a numeric vector
rs9
a numeric vector
rs10
a numeric vector
rs11
a numeric vector
rs12
a numeric vector
rs13
a numeric vector
rs14
a numeric vector
rs15
a numeric vector
rs16
a numeric vector
rs17
a numeric vector
rs18
a numeric vector
rs19
a numeric vector
rs20
a numeric vector
rs21
a numeric vector
rs22
a numeric vector
rs23
a numeric vector
rs24
a numeric vector
rs25
a numeric vector
rs26
a numeric vector
rs27
a numeric vector
rs28
a numeric vector
rs29
a numeric vector
rs30
a numeric vector
Details
A pedigree file with 20 individuals from two families. The first column is a family ID, the second an individual ID, the 3rd gives their father, the 4th their mother, and the 5th their sex. The 6th column gives their phenotype and columns 7 through 36 give their genotype, 30 SNP loci.
Source
This is synthetically generated data.
Examples
data(sample.ped.geno)
library(kinship2)
sample.ped.geno$FA[sample.ped.geno$FA == "0"] <- NA
sample.ped.geno$MO[sample.ped.geno$MO == "0"] <- NA
sample.ped.geno$Phenotype[sample.ped.geno$Phenotype >= 0] <- 1
sample.ped.geno$Phenotype[sample.ped.geno$Phenotype < 0] <- 0
ped.list <- pedigree(id = sample.ped.geno$IID, dadid = sample.ped.geno$FA,
momid = sample.ped.geno$MO, sex = sample.ped.geno$SEX,
famid = sample.ped.geno$FID,
affected = sample.ped.geno$Phenotype)
ped1 <- ped.list[1]
ped2 <- ped.list[2]
plot(ped1)
plot(ped2)