Question: R: How to test for trend of risk scores
gravatar for m93
2.6 years ago by
m93200 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.


risk scores trend test R • 1.3k views
ADD COMMENTlink modified 2.5 years ago by Biostar ♦♦ 20 • written 2.6 years ago by m93200

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


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

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by Nicolas Rosewick8.7k
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