Finding markers of all cluster using a loop

[arturomarin]

Hi,
I am new with Seurat and with R, but I have some programming skill. I am try to do the identification of conserved cell type markers for all the clusters using a for loop, but it doesn't work. The loop is:

for (i in AllClus) {
DefaultAssay(immune.combined) <- "RNA"
gmarker <- paste("g", i, sep = "")
gmarker.markers <- FindConservedMarkers(immune.combined, ident.1 = i, grouping.var = "Condition", verbose = FALSE)
}

where "AllClus" is an array that have the number of all the cluster in the data (0, 1, 2 ....). But, when I use this code the variable g0.markers, g1.markers ... don't exist. Only exist gmarker.markers variable. Someone can help me?

[timoast]

gmarker is not used here, and gmarker.markers is overwritten at each iteration of the loop. I think you might have intended to append the markers to a list, eg:

DefaultAssay(immune.combined) <- "RNA"
all_markers <- list()
for (i in AllClus) {
    gmarker <- paste("g", i, sep = "")
    all_markers[[gmarker]] <- FindConservedMarkers(immune.combined, ident.1 = i, grouping.var = "Condition", verbose = FALSE)
}

[arturomarin]

Hi,

it seems this do not work. Before your code I did:

AllClus <- c(0,1)

And when I use your code the markers of the g0 cluster do not exist:

> gmarkers[0]
character(0)
> gmarkers[1]
[1] "g1"
> gmarkers[2]
[1] NA

Any suggestion?

[Pancreas-Pratik]

Hi @arturomarin,

I do something similar like this all the time.

Try this:

for (i in AllClus) {
  DefaultAssay(immune.combined) <- "RNA"
  gmarker.markers <- FindConservedMarkers(immune.combined, ident.1 = i, grouping.var = "Condition", verbose = FALSE)
  assign(paste0("g", i, ".markers"), gmarker.markers)
  }
#cleanup environment
rm("gmarker.markers", "AllClus")

Hope this helps!

[arturomarin]

Hi @Pancreas-Pratik your script works. Thank you very much!!