1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
|
#' @importFrom stats runmed
#' @export
DM <- function(mean, cv2, win.size=51)
# Computes the distance to median for the CV2 values across all genes,
# after fitting an abundance-dependent trend.
#
# written by Jong Kyoung Kim
# with modifications by Aaron Lun
# created 12 March 2015
{
keep <- mean > 0 & !is.na(cv2) & cv2 > 0
mean.expr <- log10(mean[keep])
cv2.expr <- log10(cv2[keep])
o <- order(mean.expr)
if (win.size%%2L==0L) {
win.size <- win.size+1L
}
med.trend <- runmed(cv2.expr[o], k=win.size)
med.trend[o] <- med.trend
dm.out <- cv2.expr - med.trend
DM <- rep(NA_real_, length(keep))
DM[keep] <- dm.out
names(DM) <- names(mean)
DM
}
|
