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* '''hwe.ctrl.cutoff''' Cutoffs of HWE p-values using controls; Variants with HWE p-value smaller than the cutoffs are removed from subsequent analysis and labelled as missing; In case control studies, it is recommended to use hwe.ctrl.cutoff, since large effect variants may violate HWE.
* '''hwe.ctrl.cutoff''' Cutoffs of HWE p-values using controls; Variants with HWE p-value smaller than the cutoffs are removed from subsequent analysis and labelled as missing; In case control studies, it is recommended to use hwe.ctrl.cutoff, since large effect variants may violate HWE.
* '''max.VT''' The maximum number of thresholds used in VT; Setting max.VT to 10 can improve the speed for calculation without affecting the power too much. The default parameter is NULL, which does not set upper limit on the number of variable frequency threhsold.
* '''max.VT''' The maximum number of thresholds used in VT; Setting max.VT to 10 can improve the speed for calculation without affecting the power too much. The default parameter is NULL, which does not set upper limit on the number of variable frequency threhsold.
== Conditional Meta-analysis ==
conditional.rareMETALS2.single <- function(candidate.variant.vec,score.stat.file,cov.file,known.variant.vec,maf.cutoff,no.boot=10000,alternative=c('two.sided','greater','less'),
ix.gold=1,out.digits=4,callrate.cutoff=0,hwe.cutoff=0,hwe.ctrl.cutoff=0,p.value.known.variant.vec=NA,anno.known.variant.vec=NA,anno.candidate.variant.vec=NA)
* '''candidate.variant''' Position of candidate variant
* '''score.stat.file''' Files of score statistics
* '''cov.file''' Covariance matrix files
* '''known.variant.vec''' Range of candidate variant, expressed in a vector, e.g. c("1:12345","1:234567");
* '''test''' test of rare variant tests
* '''maf.cutoff''' Cutoffs of MAF used for determining rare variants
* '''alternative''' Alternative hypothesis to be tested
* '''out.digits''' The number of digits used in the output
* '''callrate.cutoff''' Cutoff of call rates. Sites with callrates lower than the cutoff will be labeled as missing
* '''hwe.cutoff''' Cutoff of HWE p-values. Sites with HWE pvalues lower than the cutoff will be labeled as missing
