scmageck_lr: Use linear regression to test the association of gene...

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

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, SIGNATURE = NULL, SAVEPATH = "./",LAMBDA=0.01,GENE_FRAC=0.01,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.
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 (in raw count table) are kept. If raw count table is not found, will look into scaled expression, and only keep genes whose expression is greater than zero in at least that fraction of cells. Default: 0.01.
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 this parameter for applying LR model for the 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

If SIGNATURE is set as NULL (default): returns a list of lr results, including: beta score (as a data.frame), the associated p value (as a data.frame), and the regression matrix that is used for linear regression.

If SIGNATURE is set: returns a list of signature results, including: signature result (as a data.frame), and the regression matrix that is used for linear regression.

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', SIGNATURE = NULL,
            NEGCTRL = 'NonTargetingControlGuideForHuman', PERMUTATION = 1000, SAVEPATH=NULL, LAMBDA=0.01)
    lr_score <- lr_result[1]
    lr_score_pval <- lr_result[2]
    head(lr_score_pval)

weililab/scMAGeCK documentation built on Dec. 3, 2023, 11:18 p.m.