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suchestoncampbelllab / gwasurvivr

GWAS Survival Package in R
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number of SNPs analyzed in total is blank at the end of analysis #25

Open tesselgalesloot opened 1 year ago

tesselgalesloot commented 1 year ago

Hello,

Thank you for developing gwasurvivr! I ran several chromosomes with gwasurvivr, but I noticed that at the end of analysis, where a kind of summary is provided, there is only a blank for the number of SNPs analyzed in total. See example chr22 below (one but last line).

Is this a known missing value or should I do something to obtain this value? Of course I can count the output lines of the .coxph file, but it would be convenient to check the number here. I used gwasurvivr 1.14.0.

Analyzing chunk 4141000-4142000 Analysis completed on 2022-11-02 at 14:35:14 3995983 SNPs were removed from the analysis for not meeting the threshold criteria. List of removed SNPs can be found in gwas_bcg_urolife_set1_recur_chr22.snps_removed SNPs were analyzed in total The survival output can be found at gwas_bcg_urolife_set1_recur_chr22.coxph

tesselgalesloot commented 1 year ago

Just to add, I have now performed several analyses on different cohorts, and it happens for chr1-9, 11-19 and 22, so NOT for chr10, chr20 and chr21. Minor thing, but would be nice to solve for a next version.

aarizvi commented 1 year ago

Unfortunately I’m not heavily maintaining this project as it was apart of my PhD studies, which concluded several years ago.

which function are you experiencing this with?

tesselgalesloot commented 1 year ago

I am using "michiganCoxSurv"

tesselgalesloot commented 1 year ago

It is a minor thing, maybe just something to fix if you will be updating anyway