I appreciate the development of the program
I was running a test run to understand what the flip dosage option does (which I believe it flips the A0 and A1 A0 is minor allele in the bfile?) and faced the error.
The issue maybe seems to be deriving from the package configuration?
Below are my code and error output
Dear developers,
I appreciate the development of the program I was running a test run to understand what the flip dosage option does (which I believe it flips the A0 and A1 A0 is minor allele in the bfile?) and faced the error. The issue maybe seems to be deriving from the package configuration? Below are my code and error output
plinkCoxSurv( bed.file=bed.YAOSP.OE, covariate.file=phenoCovar.YAOSP.OE, id.column='MMSID', time.to.event='YAOSP', event='Status', covariates=c('YOB', 'AAO', 'PC1', 'PC2','PC3', 'PC4'), inter.term=NULL, print.covs='only', out.file = '/castor/project/proj/soujin/TimeP/YAOSP_OE_240604', chunk.size=10000, maf.filter=NULL, clusterObj=c1, flip.dosage=F, verbose=T )
Analyzing part 2080/2081... Analyzing part 2081/2081... Error in rowVars(x, rows = rows, cols = cols, na.rm = na.rm, refine = refine, : Argument 'dim.' must be an integer vector of length two. Calls: plinkCoxSurv ... loadProcessWrite.PlinkGdsImpute2CoxSurv -> runOnChunks -> rowSds -> rowVars
Thanks for your help in advance