selectPlot {scMAGeCK} | R Documentation

## 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")

[Package scMAGeCK version 1.6.0 Index]