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]