text: user4600: I have a group of cells that have yellow (EYFP) expression and cells that don't. I want to define the yellow and non-yellow genes in two cell identities.
  I clustered the cells and then created Violin Plot for EYFP expression. Then I did FindMarkers between clusters that express high EYFP with low EYFP expression. However, this is not a very accurate way to isolate cells of high and low EYFP expression. I need to use ident to separate EYFP +ve and EYFP -ve cells (but don't know the exact syntax). Then FindMarkers between these two new identities.
  I need to subset a certain set of barcodes that express a marker gene (in this case Olfm4).
  
  user678: You have to define your ident it has to have the structure of a table. You put the cell names as names and clusters as value (for instance cell 1 = YEPF+ cell 2 = YEFP-):
  pident=as.factor(clusters)
  names(pident)=cellNames    
  object1@ident=pident
  
  Then you can run the FindAllMarkers function on this object:
  FindAllMarkers(object1, min.pct = 0.25, min.diff.pct = 0.25)
  
  
original_text: 4600: <p>I have a group of cells that have yellow (EYFP) expression and cells that don't. I want to define the yellow and non-yellow genes in two cell identities.</p>
  
  <p>I clustered the cells and then created Violin Plot for EYFP expression. Then I did FindMarkers between clusters that express high EYFP with low EYFP expression. However, this is not a very accurate way to isolate cells of high and low EYFP expression. I need to use ident to separate EYFP +ve and EYFP -ve cells (but don't know the exact syntax). Then FindMarkers between these two new identities.</p>
  
  <p>I need to subset a certain set of barcodes that express a marker gene (in this case Olfm4).</p>
   678: <p>You have to define your <code>ident</code> it has to have the structure of a table. You put the cell names as names and clusters as value (for instance cell 1 = YEPF+ cell 2 = YEFP-):</p>
  
  <pre><code>pident=as.factor(clusters)
  names(pident)=cellNames    
  object1@ident=pident
  </code></pre>
  
  <p>Then you can run the <code>FindAllMarkers</code> function on this object:</p>
  
  <pre><code>FindAllMarkers(object1, min.pct = 0.25, min.diff.pct = 0.25)
  </code></pre>
  