sample.ped.geno: Sample Pedigree Genotype Data
In famSKATRC: Family Sequence Kernel Association Test for Rare and Common Variants
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
1
data("sample.ped.geno")
Format
A data frame with 20 observations on the following 36 variables.
FIDa numeric vector
IIDa character vector
FAa character vector
MOa character vector
SEXa numeric vector
Phenotypea numeric vector
rs1a numeric vector
rs2a numeric vector
rs3a numeric vector
rs4a numeric vector
rs5a numeric vector
rs6a numeric vector
rs7a numeric vector
rs8a numeric vector
rs9a numeric vector
rs10a numeric vector
rs11a numeric vector
rs12a numeric vector
rs13a numeric vector
rs14a numeric vector
rs15a numeric vector
rs16a numeric vector
rs17a numeric vector
rs18a numeric vector
rs19a numeric vector
rs20a numeric vector
rs21a numeric vector
rs22a numeric vector
rs23a numeric vector
rs24a numeric vector
rs25a numeric vector
rs26a numeric vector
rs27a numeric vector
rs28a numeric vector
rs29a numeric vector
rs30a 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
1
2
3
4
5
6
7
8
9
10
11
12
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14
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 May 1, 2019, 9:45 p.m.
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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
1 | data("sample.ped.geno")
|
Format
A data frame with 20 observations on the following 36 variables.
FIDa numeric vector
IIDa character vector
FAa character vector
MOa character vector
SEXa numeric vector
Phenotypea numeric vector
rs1a numeric vector
rs2a numeric vector
rs3a numeric vector
rs4a numeric vector
rs5a numeric vector
rs6a numeric vector
rs7a numeric vector
rs8a numeric vector
rs9a numeric vector
rs10a numeric vector
rs11a numeric vector
rs12a numeric vector
rs13a numeric vector
rs14a numeric vector
rs15a numeric vector
rs16a numeric vector
rs17a numeric vector
rs18a numeric vector
rs19a numeric vector
rs20a numeric vector
rs21a numeric vector
rs22a numeric vector
rs23a numeric vector
rs24a numeric vector
rs25a numeric vector
rs26a numeric vector
rs27a numeric vector
rs28a numeric vector
rs29a numeric vector
rs30a 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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | 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)
|
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