assign_cell_identity: Assign single cell identity to genes to be perturbed.

In weililab/scMAGeCK: Identify genes associated with multiple expression phenotypes in single-cell CRISPR screening data

Assign single cell identity to genes to be perturbed.

Description

assign the identity of single cells, by adding a gene column to the metadata.

Usage

assign_cell_identity(BARCODE, RDS, ASSIGNMETHOD='unique') 

Arguments

BARCODE	A txt file to include cell identity information, generated from the cell identity collection step; or a corresponding data.frame.
RDS	RDS object from the pre-processRDS step; or a path to RDS file.
ASSIGNMENTMETHOD	Determine the way to assign cell identity. "unique" only assigns single cells that only have 1 guide detected (others are labeled as NA or doublet). "largest" will assign single cells with the largest umi count.

Examples

    
    ### Loading required package
    require(Seurat)
    
    ### BARCODE file contains cell identity information, generated from the cell identity collection step
    BARCODE <- system.file("extdata","barcode_rec.txt",package = "scMAGeCK")
    
    ### RDS can be a Seurat object or local RDS file path that contains the scRNA-seq dataset
    RDS <- system.file("extdata","singles_dox_mki67_v3.RDS",package = "scMAGeCK")
    
    ### For using the featurePlot function, it needs to do the preprocessRDS first
    RDS <- assign_cell_identity(BARCODE, RDS)


    

weililab/scMAGeCK documentation built on April 21, 2024, 10:36 a.m.