selectPlot: generate the selection plot

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

generate the selection plot

Description

detect the gene regulation relationship between genes and perturbation by using RRA or LR test.

Usage

selectPlot(GENE = NULL, lr_result = NULL, CUTOFF = 0.05, ADJ = "fdr", 
RRA_re1 = NULL, RRA_re2 = NULL, TYPE = select.type, QUALITY = 10)

select.type
#c("lr", "rra")

Arguments

GENE	Genes whose expressions are to be tested under the LR test. Multiple genes can be provided, separated by ",". For example, "MKI67,TP53"
lr_result	The result from the scmageck-lr step.
CUTOFF	Determine the significant pvalue.
ADJ	P.adjust.methods. Choose one of correction method. c("holm","hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none")
RRA_re1	RRA result from the scmageck-rra step.
RRA_re2	Optional input. The second RRA result from the scmageck-rra step. Add this input to visualize gene selection under two different cell condition.
TYPE	The type of the scMAGeCK results. Can be either "rra" or "lr".
QUALITY	The number of single-cells that passes the threshold when use the RRA test, default is 10. Lower quality could improve the sensitivity but reduce accuracy.

Examples

    ### by using RRA test, take MKI67 for example
    ### only works if you have RRA installed
    #selectPlot(RRA_re1 = rra_result, CUTOFF = 0.05, QUALITY = 10, ADJ = "fdr", TYPE = "rra")
    
    ### by using LR test, take MKI67 for example
    
    ### 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)
    selectPlot(GENE = "MKI67", lr_result = lr_result, CUTOFF = 0.05, ADJ = "fdr", TYPE = "lr")

weililab/scMAGeCK documentation built on April 21, 2024, 10:36 a.m.