pheno.dat {SimHap}R Documentation

Example phenotypic data

Description

pheno.dat is an example phenotypic data set containing biological measures to be used by snp.quant, haplo.quant, snp.bin and haplo.bin

Usage

data(pheno.dat)

Format

A data frame with 180 observations on the following 16 variables.

ID
patient identifiers.
SEX
1=male, 0=female.
AGE
age in years.
SBP
systolic blood pressure (mmHg).
DBP
diastolic blood pressure (mmHg).
BMI
body-mass index.
WHR
waist-hip ratio.
HDL
plasma high density lipoprotein (mmol/L).
LDL
plasma low density lipoprotein (mmol/L).
DIABETES
a binary indicator of history of type 2 diabetes.
FH_IHD
a binary indicator of family history of ischaemic heart disease.
PLAQUE
a binary indicator of the presence of 1 or more carotid plaques.
SMOKE
a binary indicator of smoking history (0=never smoked, 1=ever smoked).
PY
pack-years of smoking.
DISEASE
a binary indicator of ischaemic heart disease.
STRAT
a matching variable indicating the pairs of matched cases and controls.

Details

pheno.dat is a simulated data set of coronary heart disease related phenotypes

Examples


data(SNP.dat)

# convert SNP.dat to format required by snp.quant
geno.dat <- SNP2Geno(SNP.dat, baseline=c("MM", "11", "GG", "CC"))

data(pheno.dat)

mymodel <- snp.quant(formula1=LDL~AGE+SBP+factor(SNP_1_add),
        formula2=HDL~AGE+SBP, geno=geno.dat, pheno=pheno.dat)
summary(mymodel)

# example with a subsetting variable, looking at males only
mymodel <- snp.quant(formula1=LDL~AGE+SBP+factor(SNP_1_add),
        formula2=HDL~AGE+SBP, geno=geno.dat, pheno=pheno.dat, 
        sub=expression(SEX==1))
 

[Package SimHap version 1.0.0 Index]