Seurat QC Metrics For Each Cluster and Cluster Composition

Question

[hamindigoblue]

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.

[jared.andrews07]

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.

Answer 1

[igor]

All of the QC metrics and cluster assignments are stored in [e-mail], 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.