Closed liorlobel closed 4 months ago
Hi @liorlobel, thanks for your interest in einprot
.
You can extract the principal components from the returned SingleCellExperiment
object, e.g. for PC1:
sce <- readRDS(<path to output SCE object from einprot>)
pc1 <- reducedDims(sce)[[1]][, "PC1"]
(or even better, replace [[1]]
by [[XXX]]
, where XXX
is the name of the reduced dimension representation you want to use).
Then you can run e.g. adonis2()
or anosim()
on the returned scores and a sample grouping.
If you would like to include the results in the einprot
report, you would have to
einprot
(it will be in the extdata/
folder in the installed package location)templateRmd
argument of the run*Analysis()
functions.
Hi, thanks for this amazing package and pipeline,
I have a rather basic question. How to add/calculate a p value based on adonis or anosim for the PCA analysis?
Thanks,
Lior