<p><code>Seurat</code> objects have various <code>slot</code>s where different types and forms of data are stored. For <code>FateID</code> you would need an expression matrix (with cells as columns and genes as rows) and this can be extracted via:</p>

<pre><code>seurat_object@assays$RNA@data
</code></pre>

<p>Here <code>RNA</code> is the assay (you can have multiple assays per sample, RNA, protein, ...) and <code>data</code> is normalized data. You can extract counts or scaled data instead.</p>

<p>If you are using <code>Seurat v2</code>, drop the <code>@assays$RNA</code> part.</p>

CC BY-SA 4.0
2019-10-19T03:12:28.323Z
Dear haci, thx, I will try.
tqh003
CC BY-SA 4.0
2019-12-22T02:02:04.440Z
Thank you @haci, I have figured out it by myself.
tqh003
CC BY-SA 4.0
2019-10-09T17:00:45.683Z
2019-10-22T21:06:04.120Z
2019-10-22T21:06:04.120Z
haci
<p>I am currently using Seurat to do the scRNA-seq clustering analysis. After this, I am planning to use FateID to do the downstream analysis, could someone teach me how to convert or extract a Seurat object as the input for FateID?</p>

<p>Thanks in advance.</p>

<single-cell>
Convert or extract Seurat object as the input of FateID
# Convert or extract Seurat object as the input of FateID

(Asked by: username_0 on 2019-10-09)

I am currently using Seurat to do the scRNA-seq clustering analysis. After this, I am planning to use FateID to do the downstream analysis, could someone teach me how to convert or extract a Seurat object as the input for FateID?

Thanks in advance.

**Tags:** single-cell

---

## 1 answers

### Answer by username_1 on 2019-10-09. Score: 1

Seurat objects have various slots where different types and forms of data are stored. For FateID you would need an expression matrix (with cells as columns and genes as rows) and this can be extracted via:
seurat_object@assays$RNA@data

Here RNA is the assay (you can have multiple assays per sample, RNA, protein, ...) and data is normalized data. You can extract counts or scaled data instead.
If you are using Seurat v2, drop the @assays$RNA part.

> **Comments:**
> **username_0**: Dear haci, thx, I will try.  
> **username_0**: Thank you @haci, I have figured out it by myself.  

---

