scmageck_rra {scMAGeCK}R Documentation

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 = "./")

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.

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

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"
    ### 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)

[Package scMAGeCK version 1.6.0 Index]