scMAGeCK_RRA: Use RRA to test the association of gene knockout with certain...

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

Description

echo "Use RRA to test the association of gene knockout with certain marker expression"

Usage

scmageck_rra(BARCODE, RDS, GENE, RRAPATH = NULL, LABEL = NULL, NEGCTRL = NULL, 
KEEPTMP = FALSE, PATHWAY = FALSE, SAVEPATH = "./")

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.
GENE	Genes whose expressions are to be tested. Multiple genes can be provided, separated by ",". For example, "MKI67,TP53"
RRAPATH	The path to the RRA program, if RRA cannot be found in the PATH environment variable.
LABEL	The label of the output file.
NEGCTRL	The name of the negative control gene. For example, "NonTargetingControlGuideForHuman". Default is NULL (do not use any negative controls).
KEEPTMP	Keep temporary files.
PATHWAY	Treat genes in –GENE option as a pathway. In other words, the averaged expression of these genes will be used for testing.
SAVEPATH	The save path of result. Default save path is the current working directory. If you don't need save the result, set SAVEPATH as NULL.

Value

The result for object RDS

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")
    
    target_gene <- "MKI67"
    
    rra_result <- scmageck_rra(BARCODE=BARCODE, RDS=RDS, GENE=target_gene,
             LABEL='dox_mki67', NEGCTRL=NULL, KEEPTMP=FALSE, PATHWAY=FALSE, SAVEPATH=NULL)
    head(rra_result)

scMAGeCK documentation built on Nov. 8, 2020, 7:49 p.m.