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

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

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

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, 
SIGNATURE = NULL, KEEPTMP = FALSE, PATHWAY = FALSE, SAVEPATH = "./",ASSIGNMETHOD = "largest",SLOT='scale.data')

Arguments

BARCODE	A txt file to include cell identity information, generated from the cell identity collection step; or a corresponding data.frame.
RDS	A Seurat object or local RDS file path that contains the scRNA-seq dataset; or a path to RDS file. 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. Depreciated in 1.5.1.
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.
ASSIGNMETHOD	Method used to assign the sgRNA identity to each cell. Can be either unique or largest. See assign_cell_identity for more details.
SIGNATURE	A GMT text file, the format must be as follows:(1)Column 1: name of gene set; (2)Colum 2: Empty, or the information about gene set e.g. the source of the gene set; (3)Column 3 and onwards: ids of genes beloging to a particular gene set. Note that if you don't set the parameter "SAVEPATH", this parameter would create a folder called "GENE_SET"" in the current working directory to store the results from applying RRA program to do gene set analysis. Refercence:http://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats
SLOT	Use the slot in Seurat object for plot. May choose 'data', 'scale.data' or 'count'. See GetAssayData funciton in Seurat.

Value

A data frame of RRA results.

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"
    ### Set RRA executable file path or activate scmageck env if needed (see https://bitbucket.org/weililab/scmageck/src/master/)
    RRAPATH <- NULL
    
    rra_result <- scmageck_rra(BARCODE=BARCODE, RDS=RDS, GENE=target_gene, 
                               RRAPATH=RRAPATH, LABEL='dox_mki67', 
                               NEGCTRL=NULL, KEEPTMP=FALSE, SIGNATURE = NULL, 
                               PATHWAY=FALSE, SAVEPATH=NULL)
    head(rra_result)

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