pre_processRDS {scMAGeCK}

R Documentation

Integrate the imformation of sgRNA into RDS file for the further analysis.

Description

Pre-process the sgRNA count from previous step, and generate the sgRNA expression matrix.

Usage

pre_processRDS(BARCODE, RDS)

Arguments

BARCODE	A txt file to include cell identity information, generated from the cell identity collection step.
RDS	A Seurat object or local RDS file path that contains the scRNA-seq dataset. Note that the dataset has to be normalized and scaled.

Examples

    ### 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")
    
    Demo <- pre_processRDS(BARCODE = BARCODE, RDS = RDS)

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