gwasurvivr: an R package for genome-wide survival analysis
2019
Rizvi, Abbas A | Schwartz, Russell | Karaesmen, Ezgi | Morgan, Martin | Preus, Leah | Wang, Junke | Sovic, Michael | Hahn, Theresa | Sucheston-Campbell, Lara E.
To address the limited software options for performing survival analyses with millions of SNPs, we developed gwasurvivr, an R/Bioconductor package with a simple interface for conducting genome-wide survival analyses using VCF (outputted from Michigan or Sanger imputation servers), IMPUTE2 or PLINK files. To decrease the number of iterations needed for convergence when optimizing the parameter estimates in the Cox model, we modified the R package survival; covariates in the model are first fit without the SNP, and those parameter estimates are used as initial points. We benchmarked gwasurvivr with other software capable of conducting genome-wide survival analysis (genipe, SurvivalGWAS_SV and GWASTools). gwasurvivr is significantly faster and shows better scalability as sample size, number of SNPs and number of covariates increases. gwasurvivr, including source code, documentation and vignette are available at: http://bioconductor.org/packages/gwasurvivr. Supplementary data are available at Bioinformatics online.
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