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
|
modelMatrixMeth <- function(object, ...)
# Create expanded model matrix (aka design matrix) for edgeR analysis of BS-seq methylation counts.
# Gordon Smyth
# Created 26 Dec 2017.
{
# If object isn't already a design matrix, create the design matrix from treatments at the sample level
if(is.matrix(object)) {
design.treatments <- object
} else {
design.treatments <- model.matrix(object, ...)
}
# Design matrix for samples
# Allow for two observations (methylated and unmethylated counts) for each sample
nsamples <- nrow(design.treatments)
Sample <- gl(nsamples,2L)
design.samples <- model.matrix(~0+Sample)
# Expand design.treatments for meth & unmeth counts
design.treatments <- design.treatments[as.integer(Sample),]
# Combine with treatments applying to methylation effects
Methylation <- gl(2L,1L,2L*nsamples)
cbind(design.samples, (Methylation==1L) * design.treatments)
}
|
