Question: R: How to test for trend of risk scores
1
gravatar for magda.meier
5 months ago by
magda.meier20
magda.meier20 wrote:

I have some case/control data like so (many more rows)

ID    score     phenotype
1     0.6482772         0
2     0.9519315         1
3     2.7689036         0
4     1.9974466         1
5     1.6287841         1
6     1.9993825         0

I performed a logistic regression on pheno~score to determine if an increase in scores leads to increased odds ratio (a measure of disease risk)

I now want to do a trend test in R to test whether there is trend. This trend test would just give me one odds ratio and a p-value. Does anyone know which R package or function I could use? I've looked around and I'm struggling to find a simple package that can help me do this.

Thanks

risk scores trend test R • 331 views
ADD COMMENTlink modified 5 months ago by Biostar ♦♦ 20 • written 5 months ago by magda.meier20
1

As phenotype is either 0 or 1 could you just do a fisher test as :

fisher.test(score,phenotype)

Could also be nice to plot the data as boxplots (x is the data.frame containing your data):

ggplot(x,aes(x=score,y=score))+geom_boxplot()
ADD REPLYlink modified 5 months ago • written 5 months ago by Nicolas Rosewick6.0k
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