## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(echo = TRUE) ## ----------------------------------------------------------------------------- library(scMAGeCK) ### 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") ### Set RRA executable file path. ### You can generate RRA executable file by following commands: ### wget https://bitbucket.org/weililab/scmageck/downloads/RRA_0.5.9.zip ### unzip RRA_0.5.9.zip ### cd RRA_0.5.9 ### make RRAPATH <- "/Library/RRA_0.5.9/bin/RRA" target_gene <- "MKI67" rra_result <- scmageck_rra(BARCODE=BARCODE, RDS=RDS, GENE=target_gene, RRAPATH=RRAPATH, LABEL='dox_mki67', NEGCTRL=NULL, KEEPTMP=FALSE, PATHWAY=FALSE, SAVEPATH=NULL) ## ----------------------------------------------------------------------------- library(scMAGeCK) ### 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]