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

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

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)

scMAGeCK documentation built on Nov. 8, 2020, 7:49 p.m.