Description Usage Format Source Examples
Phenotype and genotype data from the Finland United States Investigation of NIDDM (type 2) Diabetes (FUSION) study.
1 |
Data frames with the following variables.
id
subject ID number for matching between data sets
t2d
a factor with levels case
control
bmi
body mass index
sex
a factor with levels F
M
age
age of subject at time phenotypes were colelcted
smoker
a factor with levels former
never
occasional
regular
chol
total cholesterol
waist
waist circumference (cm)
weight
weight (kg)
height
height (cm)
whr
waist hip ratio
sbp
systolic blood pressure
dbp
diastolic blood pressure
marker
RS name of SNP
markerID
numeric ID for SNP
allele1
first allele coded as 1=A, 2=C, 3=G, 4=T
allele2
second allele coded as 1=A, 2=C, 3=G, 4=T
genotype
both alleles coded as a factor
Adose
number of A alleles
Cdose
number of C alleles
Gdose
number of G alleles
Tdose
number of T alleles
Similar to the data presented in
Laura J. Scott, Karen L. Mohlke, Lori L. Bonnycastle, Cristen J. Willer, Yun Li, William L. Duren, Michael R. Erdos, Heather M. Stringham, Pe- ter S. Chines, Anne U. Jackson, Ludmila Prokunina-Olsson, Chia-Jen J. Ding, Amy J. Swift, Narisu Narisu, Tianle Hu, Randall Pruim, Rui Xiao, Xiao- Yi Y. Li, Karen N. Conneely, Nancy L. Riebow, Andrew G. Sprau, Maurine Tong, Peggy P. White, Kurt N. Hetrick, Michael W. Barnhart, Craig W. Bark, Janet L. Goldstein, Lee Watkins, Fang Xiang, Jouko Saramies, Thomas A. Buchanan, Richard M. Watanabe, Timo T. Valle, Leena Kinnunen, Goncalo R. Abecasis, Elizabeth W. Pugh, Kimberly F. Doheny, Richard N. Bergman, Jaakko Tuomilehto, Francis S. Collins, and Michael Boehnke, A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility vari- ants, Science (2007).
1 2 3 4 5 6 7 | data(pheno); data(fusion1); data(fusion2)
fusion1m <- merge(fusion1, pheno, by="id", all.x=FALSE, all.y=FALSE)
xtabs(~t2d + genotype, fusion1m)
xtabs(~t2d + Gdose, fusion1m)
chisq.test( xtabs( ~t2d + genotype, fusion1m ) )
f1.glm <- glm( factor(t2d) ~ Gdose, fusion1m, family=binomial)
summary(f1.glm)
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