hi
thank you so much for the suggestion! I agree with you that a function that organizes the output of sortGenes and getPValues together in a single tidy table is a nice idea and I will update this issue as soon as I have written it.

Until then, please see below and feel free to post any further questions!

the specScore matrix can be used to rank genes in each clusters, to estimate a cutoff to get all variable (differentially expressed genes, DEGs) I would go for the "adjpval" matrix from getPValues.

if "sg" is the output of "sortGenes()", this will give you the top 10 genes in each cluster:
plotTopMarkerHeat(sg, top_n = 10, outs = TRUE, plotheat = FALSE)

to get a small set of marker genes:
getMarkers(sg)

To get all variable genes:
pp=getPValues(sg)
names(which(apply(pp$adjpval, 1, function(x) any(x < 0.05))))

to get all marker genes for say cluster 1:
rownames(pp$adjpval[which(pp$adjpval[,1] < 0.05),])

Thanks for the prompt reply, actually, I have already done what you said.
Again, It is really a fast method, I really like it!

Best wishes,

Zorro

hi

there is now a new function in the latest release called getTable to summarize variable genes and fold change values. I would recommend now to run something like this to get all variable genes:

gs = sortGenes(kidneyTabulaMuris$exp, kidneyTabulaMuris$cellType)
pp = getPValues(gs)
tab = getTable(gs, pp)

to get a small list of marker genes:
mm = getMarkers(gs)

I'm closing the issue now, however feel free to reopen or open a new one if you have any further questions.

best wishes
Mahmoud