Changes

From Genome Analysis Wiki
Jump to: navigation, search

RareMETALS2

2,707 bytes added, 21:04, 14 June 2015
no edit summary
* ''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 ==
 
rareMETALS2.range <- function(score.stat.file,cov.file,range,range.name,test='GRANVIL',maf.cutoff=1,alternative=c('two.sided','greater','less'),ix.gold=1,out.digits=4,callrate.cutoff=0,hwe.cutoff=0,hwe.ctrl.cutoff=0,max.VT=NULL)
 
* '''score.stat.file''' files of score statistics
* '''cov.file''' covariance matrix files
* '''range''' tabix range for each gene/region
* '''range.name''' The name of the range,e.g. gene names can be used
* '''test''' rare variant tests to be used
* '''maf.cutoff''' MAF cutoff used to analyze variants
* '''alternative''' alternative hypothesis to be specified
* '''ix.gold''' Gold standard population to align reference allele to
* '''out.digits''' Number of digits used in the output
* '''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.
* '''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.
131
edits

Navigation menu