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RareMETALS2

1,593 bytes added, 21:58, 14 June 2015
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I have created a '''google group''' for discussion on the usage and for bug reports etc. If you find any issues to the package and think that the discussions may also benefit others, please post them to the user group. Here is the link to the discussion group https://groups.google.com/forum/#!forum/raremetals
 
== 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)
* ''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.
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