scmageck_rra {scMAGeCK} | R Documentation |
echo "Use RRA to test the association of gene knockout with certain marker expression"
scmageck_rra(BARCODE, RDS, GENE, RRAPATH = NULL, LABEL = NULL, NEGCTRL = NULL, SIGNATURE = NULL, KEEPTMP = FALSE, PATHWAY = FALSE, SAVEPATH = "./")
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. |
GENE |
Genes whose expressions are to be tested. Multiple genes can be provided, separated by ",". For example, "MKI67,TP53" |
RRAPATH |
The path to the RRA program, if RRA cannot be found in the PATH environment variable. |
LABEL |
The label of the output file. |
NEGCTRL |
The name of the negative control gene. For example, "NonTargetingControlGuideForHuman". Default is NULL (do not use any negative controls). |
KEEPTMP |
Keep temporary files. |
PATHWAY |
Treat genes in –GENE option as a pathway. In other words, the averaged expression of these genes will be used for testing. |
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. |
SIGNATURE |
A GMT text file, the format must be as follows:(1)Column 1: name of gene set; (2)Colum 2: Empty, or the information about gene set e.g. the source of the gene set; (3)Column 3 and onwards: ids of genes beloging to a particular gene set. Note that if you don't set the parameter "SAVEPATH", this parameter would create a folder called "GENE_SET"" in the current working directory to store the results from applying RRA program to do gene set analysis. Refercence:http://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats |
The result for object RDS
### 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") target_gene <- "MKI67" ### Set RRA executable file path or activate scmageck env if needed (see https://bitbucket.org/weililab/scmageck/src/master/) RRAPATH <- NULL rra_result <- scmageck_rra(BARCODE=BARCODE, RDS=RDS, GENE=target_gene, RRAPATH=RRAPATH, LABEL='dox_mki67', NEGCTRL=NULL, KEEPTMP=FALSE, SIGNATURE = NULL, PATHWAY=FALSE, SAVEPATH=NULL) head(rra_result)