Question: Seurat QC Metrics For Each Cluster and Cluster Composition
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gravatar for hamindigoblue
11 months ago by
hamindigoblue0 wrote:

In the Seurat vignette, it shows how you can find QC metrics (nc_features, MT, nc_RNA, ect) for each sample. How can you find these metrics for each cluster, after you've generated the clusters?

Secondly, I couldn't find this in the manual, but how can you see the percentage of contribution that each cluster gives? For example, I want to know how much each cluster contributes to the total amount of cells that were sequenced.

seurat single cell • 634 views
ADD COMMENTlink modified 11 months ago by igor11k • written 11 months ago by hamindigoblue0

What do you mean by "how much each cluster contributes to the total amount of cells"? Just the percentage of total cells in each cluster? If so, that can be derived easily just by counting the number of cells in each cluster from the metadata dataframe as described by igor.

ADD REPLYlink written 11 months ago by jared.andrews077.9k
0
gravatar for igor
11 months ago by
igor11k
United States
igor11k wrote:

All of the QC metrics and cluster assignments are stored in seurat_obj@meta.data, which is a standard data frame. If you are comfortable working with data frames, then you don't need any specialized functions to extract summary statistics.

ADD COMMENTlink modified 11 months ago • written 11 months ago by igor11k
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