Nothing
##########################################################################
#transformations
#
# x: One value per gene gained from gene level statistic.
#
# A collection of methods which can be used to transform the gene level
# statistic.
##########################################################################
transformation.abs <- function(x){
tmp <- abs(x)
names(tmp) <- names(x)
return(tmp)
}
transformation.square <- function(x){
tmp <- x^2
names(tmp) <- names(x)
return(tmp)
}
transformation.localFdr <- function(x,
statistic="pvalue",
cutoff.method="fndr",
pct0=0.75){
requireNamespace("fdrtool")
tmp <- fdrtool::fdrtool(x,
statistic = statistic,
cutoff.method = cutoff.method,
pct0 = pct0,
plot=FALSE,
verbose = FALSE)$lfdr
names(tmp) <- names(x)
return(tmp)
}
transformation.binarize <- function(x, quant = 0.95){
tmp <- rep(0, length(x))
tmp[x > quantile(x, prob = quant)] <- 1
names(tmp) <- names(x)
return(tmp)
}
transformation.rank <- function(x){
tmp <- rank(x)
names(tmp) <- names(x)
return(tmp)
}
transformation.adjust <- function(x, adjMethod = "fdr"){
tmp <- p.adjust(x, method = adjMethod)
names(tmp) <- names(x)
return(tmp)
}
transformation.adjustAndBinarize <- function(x, adjMethod = "fdr", threshold = 0.05){
tmp <- as.numeric(p.adjust(x, method = adjMethod) < threshold)
names(tmp) <- names(x)
return(tmp)
}
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