Nothing
summary.eqtl <- function(object, sig=0.01, ...){
ws <- object$windowSize
trans <- FALSE
if(is.null(ws)){
ws <- "trans-eQTL"
trans <- TRUE
}
p.values <- sapply(object$eqtl,"[",3)
if(trans){
cat("trans-EQTL Summary\n")
} else {
cat("cis-EQTL Summary\n")
}
cat("---------------\n")
cat("Type of test :",object$method,"\n")
testedGenes <- 0
if(trans){
testedGenes <- length(object$xAnnot)
} else {
testedGenes <- length(object$eqtl)
}
cat("Tested genes :",testedGenes,"\n")
cat("Total number of SNPs (in geno object) :",dim(object$geno[[3]])[1],"\n")
cat("Window size (in MB) :",ws,"\n")
if(!trans) cat("Average (median) number of SNP in window :",mean(sapply(p.values,length)),"(",median(sapply(p.values,length)),")\n")
sigP <- sapply(p.values, function(x){sum(x<=sig, na.rm=TRUE)})
if(!trans) cat("Average (median) number of sig. (p<",sig,") SNP in window :",mean(sigP),"(",median(sigP),")\n")
invisible(object)
}
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