Introduction

Current version is 0.41

GATE (Genetic Analysis of Time-to-Event phenotypes) is an R package with Scalable and accurate genome-wide association analysis of censored survival data in large scale biobanks using frailty models.

GATE performs single-variant association tests for time-to-event endpoints. GATE uses uses the saddlepoint approximation (SPA)(mhof, J. P. , 1961; Kuonen, D. 1999; Dey, R. et.al 2017) to account for heavy censoring rates.

GATE is based on joint work by Rouank Dey and Wei Zhou.

*This R package is still under development using the SAIGE github repository and will be moved to a new github repository soon.

Citation

How to install and run GATE (Similar to SAIGE and SAIGE-GENE)

https://github.com/weizhouUMICH/SAIGE/wiki/Genetic-association-tests-using-SAIGE

The github branch name is SAIGE_homN_hetN_surv The docker image can be found in the docker hub wzhou88/saige.survival:0.40.2

Notes for users before running jobs

After installation, the package needs to be called as SAIGE (will update)
Currently, the only difference between this and the regular SAIGE job is that for step1, two additional arguments are used

eventTimeCol = “”,
eventTimeBinSize = 1

and

traitType = “survival”

eventTimeCol is the column name for the event time, e.g. age of diagnosis eventTimeBinSize is used to set the bin size for evene times. eventTimeBinSize=1 means the bin size will be 1 and if eventTimeBinSize is not specified, raw event time values will be used

Logs for bug fixing

0.41 (January-11-2021) fix the error from the merging branches