selectPlot {scMAGeCK} | R Documentation |
detect the gene regulation relationship between genes and perturbation by using RRA or LR test.
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")
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. |
### 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")