Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-10-19T03:12:28.323Z
Answers.Text: Dear haci, thx, I will try.
Answers.UserDisplayName: tqh003
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-12-22T02:02:04.440Z
Answers.Text: Thank you @haci, I have figured out it by myself.
Answers.UserDisplayName: tqh003
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-10-09T17:00:45.683Z
Answers.LastActivityDate: 2019-10-22T21:06:04.120Z
Answers.LastEditDate: 2019-10-22T21:06:04.120Z
Answers.UserDisplayName: haci
Body: <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>
  
Tags: <single-cell>
Title: Convert or extract Seurat object as the input of FateID
ThreadText: # 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 `slot`s 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 username_1, thx, I will try.  
  > **username_0**: Thank you @username_1, I have figured out it by myself.  
  
  ---
  
  