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
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
|
scaleOffset <- function(y, ...)
UseMethod("scaleOffset")
scaleOffset.default <- function(y, offset, ...)
# Ensures scale of offsets are consistent with library sizes.
# Aaron Lun and Yunshun Chen.
# Created 8 Dec 2016, last modified 1 Jun 2020
{
if(is.matrix(y)) lib.size <- colSums(y)
else lib.size <- y
if(is.matrix(offset)) {
if (ncol(offset)!=length(lib.size)) {
stop("'ncol(offset)' should be equal to number of libraries")
}
if(inherits(offset,"CompressedMatrix")) {
if(attr(offset, "repeat.row")) {
adj <- mean(offset)
} else if (attr(offset, "repeat.col")) {
offset <- makeCompressedMatrix(0, dim(offset))
adj <- 0
} else {
adj <- rowMeans(as.matrix(offset))
}
} else {
adj <- rowMeans(offset)
}
} else {
if (length(offset)!=length(lib.size)) {
stop("length of 'offset' should be equal to number of libraries")
}
adj <- mean(offset)
}
mean(log(lib.size)) + offset - adj
}
scaleOffset.DGEList <- function(y, offset, ...)
# Ensures scale of offsets are consistent with library sizes.
# Aaron Lun and Yunshun Chen.
# Created 8 Dec 2016, last modified 29 May 2020
{
lib.size <- y$samples$lib.size * y$samples$norm.factors
y$offset <- scaleOffset(lib.size, offset)
y
}
|
