1) Is there a way to test the proportional hazards assumption for each covariate included in a Cox regression model fit using gwasurvivr? (e.g. cox.zph() function in survival package)
2) From output files, I found SNPs with SAMP_MAF > 0.005 in both .snps_removed file and .coxph file. (I applied the option maf.filter=0.005) I don't understand why there are SNPs with SAMP_MAF > 0.005 in .snps_removed file and the SNPs in .snp_removed file are also included in .coxph file.
Here are printed messages from the analysis:
11191 SNPs were removed from the analysis for not meeting
the given threshold criteria or for having MAF = 0
List of removed SNPs are saved to
/data1/ishim/Project/chr22.snps_removed
In total 118041 SNPs were included in the analysis
The Cox model results output was saved to
/data1/ishim/Project/chr22.coxph
Parts of chr22.snps_removed:
Parts of chr22.coxph:
I found only 4 SNPs with SAMP_MAF < 0.005 in .snp_removed files for all chromosomes as below.
Strangely, the four SNPs have different values of SAMP_MAF in .coxph files.
Can I include SNPs in .snps_removed files for my further analysis?
Hi,
I have two questions about using gwasurvivr.
1) Is there a way to test the proportional hazards assumption for each covariate included in a Cox regression model fit using gwasurvivr? (e.g. cox.zph() function in survival package)
2) From output files, I found SNPs with SAMP_MAF > 0.005 in both .snps_removed file and .coxph file. (I applied the option maf.filter=0.005) I don't understand why there are SNPs with SAMP_MAF > 0.005 in .snps_removed file and the SNPs in .snp_removed file are also included in .coxph file.
Here are printed messages from the analysis:
11191 SNPs were removed from the analysis for not meeting the given threshold criteria or for having MAF = 0 List of removed SNPs are saved to /data1/ishim/Project/chr22.snps_removed In total 118041 SNPs were included in the analysis The Cox model results output was saved to /data1/ishim/Project/chr22.coxph
Parts of chr22.snps_removed:
Parts of chr22.coxph:
I found only 4 SNPs with SAMP_MAF < 0.005 in .snp_removed files for all chromosomes as below.
Strangely, the four SNPs have different values of SAMP_MAF in .coxph files.
Can I include SNPs in .snps_removed files for my further analysis?
Thank you so much for your help!