MASTDETest: Differential expression using MAST
In tangchao7498/ICAS:

Description Usage Arguments Details Value References

View source: R/differential_expression_external.R

Identifies differentially expressed SJs between two groups of cells using a hurdle model tailored to scRNA-seq data. Utilizes the MAST package to run the DE testing.

1	MASTDETest(object, cells.1, cells.2, genes.use = NULL, ...)

`object`	ICASDataSet object
`cells.1`	Group 1 cells
`cells.2`	Group 2 cells
`genes.use`	SJs to use for test
`...`	Additional parameters to zero-inflated regression (zlm) function in MAST
`latent.vars`	Confounding variables to adjust for in DE test. Default is "nUMI", which adjusts for cellular depth (i.e. cellular detection rate). For non-UMI based data, set to nGene instead.

To use this method, please install MAST, using instructions at https://github.com/RGLab/MAST/

Returns a p-value ranked matrix of putative differentially expressed SJs.

Andrew McDavid, Greg Finak and Masanao Yajima (2017). MAST: Model-based Analysis of Single Cell Transcriptomics. R package version 1.2.1. https://github.com/RGLab/MAST/

tangchao7498/ICAS documentation built on Jan. 28, 2021, 3:56 p.m.