sample.ped.geno: Sample Pedigree Genotype Data

Description Usage Format Details Source Examples

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

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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

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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)

famSKATRC documentation built on Nov. 17, 2017, 4:42 a.m.