pacoxph and R yield different results

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Posts: 5
Joined: Fri Apr 25, 2014 3:21 pm

pacoxph and R yield different results

Postby jal » Thu May 08, 2014 10:36 am

I got different answers from pacoxph and R for interaction analysis. For example, using the ProbABEL example data "coxph_data.txt", we do age*SNP interaction test. The pacoxph command is

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pacoxph -p coxph_data.txt -d gtdata/test.mldose -i gtdata/test.mlinfo -m gtdata/ -c 19 -o Ocoxph_int --interaction=2

output for first SNP:

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name A1 A2 Freq1 MAF Quality Rsq n Mean_predictor_allele chrom position beta_SNP_add sebeta_SNP_add beta_SNP_age sebeta_SNP_age chi2_SNP
rs7247199 GAC A 0.5847 0.415 0.9299 0.8666 200 0.333517 19 204938 0.618349 20.3844 0.0271815 0.0157229 0.0268377

Now, we combine "coxph_data.txt" and "gtdata/test.mldose" in R

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phe<-read.table("coxph_data.txt", header=T)
gen<-read.table("gtdata/test.mldose", header=F)
dat=cbind(phe, gen)

Let's take the first SNP rs7247199 and run the same cox mdoel in R

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coxph(Surv(fupt_chd ,chd) ~ age * rs7247199 + sex + othercov, data=dat)


Code: Select all

coxph(formula = Surv(fupt_chd, chd) ~ age * rs7247199 + sex + othercov, data = dat)

                  coef exp(coef) se(coef)      z       p
age            -0.6365  5.29e-01    1.179 -0.540 5.9e-01
rs7247199     -50.3502  1.36e-22   97.108 -0.518 6.0e-01
sex             2.3016  9.99e+00    0.402  5.728 1.0e-08
othercov        0.0923  1.10e+00    0.139  0.663 5.1e-01
age:rs7247199   0.9835  2.67e+00    1.772  0.555 5.8e-01

Likelihood ratio test=59.6  on 5 df, p=1.46e-11  n= 200, number of events= 64

You can see the results are very different. Did I do something wrong?


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