How to use WhichCells Function to label clusters

Question

[world]

The WhichCells function can pull the names of cells that were experimentally marked as iPS cells, and find that they have been placed in cluster 7)

ips.cells=WhichCells(nbt,"iPS",id = "orig.ident")

my.data=FetchData(nbt,"ident",cells.use = ips.cells)

head(my.data,2)

              ident

 Hi_iPS_1     7

 Hi_iPS_2     7
  

When I use the function though, the idents column do not return the cluster ID

FetchData(stemcells, c("ident", "orig.ident"))

                 ident orig.ident
old_LT_HSC_2       old        old
old_LT_HSC_3       old        old
  

Before, I've subsetted my data into control and stimulated cells. How can I get the cluster ID for all the cells?

[Haci]

Your question/post is a little bit raw but from what I understand you are using Seurat for single cell analysis. As far as I can see from your code, you are feeding different objects nbd and stemcells to WhichCells() and FetchData() respectively, I am not surprised that you get different outputs.

And for your question on how to get cluster ID, please check the @meta.data slot of your Seurat object. If I remember correctly cluster ids are stored in a column for which the column name is either prefixed our suffiexed by "res" and then the "resolution" parameter used for clustering.