Seurat -Subset Seurat objects based on gene expression

Description

This tool gives you a subset of the data: only those cells that have expression in a user defined gene. Expression threshold is given as a parameter.

Parameters

• Gene ["MS4A1"]
• Expression level threshold [1]

Details

As inputs, give a Seurat object.

Select the gene based on which you want to subset the data (as an example, this parameter is set to "MS4A1"). Then select the expression value threshold (as an exampe, this parameter is set to 1).

Output

• seurat_obj_subset.Robj: The Seurat R-object containing only the cells expressing a given gene above the threshold value. Can be passed to the next Seurat tool, or imported to R. Not viewable in Chipster.
• subset_plot.pdf: Gives the number of cells left in the subset