Nothing
`summary.ROTS` <-
function(object, fdr=NULL, num.genes=NULL, verbose=TRUE, ...){
if( !is.null(fdr) || !is.null(num.genes)){
## Sort ROTS-statistic values (abs)
sorted.rots <- abs(object$d)
names(sorted.rots) <- rownames(object$data)
sorted.rots <- sort(sorted.rots, decreasing=TRUE)
## Add feature-names to fdr and ROTS values
names(object$FDR) <- rownames(object$data)
names(object$d) <- rownames(object$data)
names(object$pvalue) <- rownames(object$data)
## Result matrix, columns are: "Row", "ROTS-statistic", "pvalue" and "FDR"
result <- numeric(0)
result <- cbind(match(names(sorted.rots), rownames(object$data)),
object$d[names(sorted.rots)],
object$pvalue[names(sorted.rots)],
object$FDR[names(sorted.rots)])
colnames( result ) <- c("Row", "ROTS-statistic", "pvalue", "FDR")
## Show only num.gene top rows or rows whose false discovery rate <= fdr
if(!is.null(fdr))
result <- result[ result[,4] <= fdr, ,drop=FALSE]
else
result <- result[ 1 : min(num.genes, nrow(result)), ,drop=FALSE]
if( verbose ){
cat("ROTS results:", "\n\n")
cat("Number of resamplings: ", object$B, "\n\n")
cat("a1: ", object$a1,"\n")
cat("a2: ", object$a2,"\n")
cat("Top list size: ", object$k, "\n")
cat("Reproducibility value: ", object$R, "\n")
cat("Z-score: ", object$Z, "\n\n")
cat(nrow(result), "rows satisfy the condition.")
## Print oly 10 first rows
if(nrow(result) > 10){
cat(" Only ten first rows are" ,"\n",
"displayed, see the return value for the whole output.\n")
print(result[1:10, ])
cat("...", "\n")
}
else{
cat("\n")
print(result)
}
}
return(invisible(result))
}
}
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