scmageck_lr {scMAGeCK} | R Documentation

## Use linear regression to test the association of gene knockout with all possible genes

### Description

echo "Use linear regression to test the association of gene knockout with all possible genes"

### Usage

    scmageck_lr(BARCODE, RDS, NEGCTRL, SELECT_GENE=NULL, LABEL = NULL,
    PERMUTATION = NULL, SAVEPATH = "./",LAMBDA=0.01,GENE_FRAC=0.01)

### 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.
`NEGCTRL` | The name of the genes (separated by ",") served as negative controls.
`SELECT_GENE` | The list of genes for regression. By default, all genes in the table are subject to regression.
`LABEL` | The label of the output file.
`PERMUTATION` | The number of permutations for p value calculation.
`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.
`LAMBDA` | A paramter for the LR model for ridge regression. Default: 0.01.
`GENE_FRAC` | A paramter for filtering low expressed genes. By default, only genes that have expressions in at least that fractions of cells are kept. Default: 0.01.

### 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")

        lr_result <- scmageck_lr(BARCODE=BARCODE, RDS=RDS, LABEL='dox_scmageck_lr',
                NEGCTRL = 'NonTargetingControlGuideForHuman', PERMUTATION = 1000, SAVEPATH=NULL, LAMBDA=0.01)
        lr_score <- lr_result[1]
        lr_score_pval <- lr_result[2]
        head(lr_score_pval)

[Package scMAGeCK version 1.4.0 Index]