Question: Extracting cells only from one condition (Seurat)
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gravatar for V
7 weeks ago by
V200
UK/London
V200 wrote:

Hello,

I've combined 3 seurat files in order to do an integrated analysis and everything is working fine, but I would like to extract some cells for subsequent analysis. As the dimplot is now, the clusters consist of cells from all of my conditions so I can not seem to do the usual approach which would be something like :

Cluster.1.8.12.only <- subset(x = seuratA, idents = c('1','8', '12'))

if for example I wanted clusters 1,8 and 12.

Does anyone know how I would modify the above to for example, get clusters 1, 8 and 12 but of only the condition I'm interested in? for simplicity sake lets assume the conditions are labelled A, B and C and are in an integrated seurat called ABC.combined.

Thank you for your help :)

ADD COMMENTlink modified 7 weeks ago by jared.andrews075.2k • written 7 weeks ago by V200
0
gravatar for jared.andrews07
7 weeks ago by
jared.andrews075.2k
St. Louis, MO
jared.andrews075.2k wrote:

I'd probably just subset again. Same approach, just using the metadata column using your condition.

Cluster.1.8.12.cond <- subset(x = Cluster.1.8.12.only, subset = your_condition_column == "condition_of_interest")
ADD COMMENTlink modified 7 weeks ago • written 7 weeks ago by jared.andrews075.2k
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