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RareMETALS2

14 bytes added, 21:05, 14 June 2015
Meta-analysis of Single Variant Associations
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''':
* '''score.stat.file''' files of score statistics * '''range tabix''' range of variants to be analyzed * '''alternative''' alternative hypothesis to be specified * '''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) * '''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.
== Meta-analysis of Gene-level Association ==
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