Extracting data from edgeR R package

Question

[Sara]

I am using edgeR package in R and here the code I used

library(edgeR)
target <-read.delim("metadata.txt", header=T)
x <- read.csv('data4.txt', row.names = 1)
group <- factor(target$group)
design <- model.matrix(~0+group)

when I print the design variable I would get the following results:

> design
   group1 group2
1       1      0
2       1      0
3       0      1
4       1      0
5       0      1
6       1      0
7       1      0
8       1      0
9       0      1
10      0      1
11      1      0
12      0      1
attr(,"assign")
[1] 1 1
attr(,"contrasts")
attr(,"contrasts")$group
[1] "contr.treatment"

I would like to make a new variable called comparison like this:

comparison = "group1-group2"

I actually do not know how to do that because group1 and group2 are not headers or separated sections. do you guys know how to that?

Answer 1

[zx8754]

Get the dimnames:

#example data
group <- factor(1:2)
design <- model.matrix(~0+group)
design 
#   group1 group2
# 1      1      0
# 2      0      1
# attr(,"assign")
# [1] 1 1
# attr(,"contrasts")
# attr(,"contrasts")$group
# [1] "contr.treatment"

paste(dimnames(design)[[2]], collapse = "-")
# [1] "group1-group2"

Answer 2

[russhh]

Hi are you trying to subtract the second column of the design from the first, you could do that with matrix manipulation: as.matrix(design) %*% c(1, -1). However, I suspect you're trying to define an experimental comparison (contrast) for use in the edgeR workflow. As such you're probably looking for limma::makeContrasts https://www.rdocumentation.org/packages/limma/versions/3.28.14/topics/makeContrasts ;

contrasts <- limma::makeContrasts(comparison = "group1 - group2", levels = design)

[Sara]

@russhh: in your solution I have to type manually but I want to make "group1 - group2" automatically. because instead of "group1 - group2" I can have: "groupA- groupB".

[russhh]

Sorry, that wasn't clear