Changes

   rareMETALS2.single <- function(score.stat.file,range,alternative=c('two.sided','greater','less'),ix.gold=1,callrate.cutoff=0,hwe.cutoff=0,hwe.ctrl.cutoff=0)

   rareMETALS2.single <- function(score.stat.file,range,alternative=c('two.sided','greater','less'),ix.gold=1,callrate.cutoff=0,hwe.cutoff=0,hwe.ctrl.cutoff=0)

'''Relevant Parameters''':

'''Relevant Parameters''':

* ''score.stat.file'' files of score statistics                                                                                                           

* '''score.stat.file''' files of score statistics                                                                                                           

* ''range tabix'' range of variants to be analyzed                                                                                                       

* '''range tabix''' range of variants to be analyzed                                                                                                       

* ''alternative'' alternative hypothesis to be specified                                                                                                 

* '''alternative''' alternative hypothesis to be specified                                                                                                 

* ''ix.gold'' Gold standard population to align reference allele to.                                                                                     

* '''ix.gold''' Gold standard population to align reference allele to.                                                                                     

* ''callrate.cutoff'' Cutoffs of call rate, lower than which will NOT be analyzed (labelled as missing)                                                   

* '''callrate.cutoff''' Cutoffs of call rate, lower than which will NOT be analyzed (labelled as missing)                                                   

* ''hwe.cutoff'' Cutoffs of HWE p-values; Variants with HWE p-value smaller than the cutoffs are removed from subsequent analysis and labelled as missing;                                                                                                                                                           

* '''hwe.cutoff''' Cutoffs of HWE p-values; Variants with HWE p-value smaller than the cutoffs are removed from subsequent analysis and labelled as missing;                                                                                                                                                           

* ''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.

== Meta-analysis of Gene-level Association ==

== Meta-analysis of Gene-level Association ==