Open denvercal1234GitHub opened 9 months ago
Q1. If I want to use
de.method="wilcox"
, would you mind giving me how to modify the code?
de.method="wilcox"
just uses genes derived from scran::findMarkers
. Basically something like:
pairwise <- pairwiseWilcox(x = ref, groups = labels, direction = "up", log.p = TRUE)
collected <- scran::getTopMarkers(pairwise$statistics, pairwise$pairs,
n = 10, pval.field = "log.p.value", fdr.field = "log.FDR", fdr.threshold = log(0.05))
lapply(collected, as.list)
(Adapted from SingleR:::.get_genes_by_de
, which is what trainSingleR
calls under the hood.)
This will give you a list of lists of markers that is comparable to the output of getClassicMarkers
.
Q2. And, is it appropriate to use com.markers from
getClassicMarkers()
in `SingleR(... de.method="wilcox"...) or really com.markers should only be used for de.method="classic"?
If you give genes=
, any setting of de.method=
will be ignored.
Hi there,
Thanks again for a great package.
In the tutorial (https://bioconductor.org/books/release/SingleRBook/using-multiple-references.html#using-harmonized-labels), the gene from references are determined via
getClassicMarkers()
for use when de.method="classic".Q1. If I want to use
de.method="wilcox"
, would you mind giving me how to modify the code?Q2. And, is it appropriate to use com.markers from
getClassicMarkers()
in `SingleR(... de.method="wilcox"...) or really com.markers should only be used for de.method="classic"?Thank you again!