MASTTest: Differential expression using MAST
In Coolgenome/iTALK: Characterize and Illustrate Intercellular Communication

Description Usage Arguments Details Value References

Identifies differentially expressed genes between two groups of cells using MAST

1
2
3

MASTTest(sub_data, min_gene_expressed, min_valid_cells,
  contrast = unique(sub_data$compare_group), method = "glm",
  silent = FALSE, check_logged = TRUE)

`sub_data`	Count data removed cell_type and selected certain two compare_group
`min_gene_expressed`	Genes expressed in minimum number of cells
`min_valid_cells`	Minimum number of genes detected in the cell
`contrast`	String vector specifying the contrast to be tested against the log2-fold-change threshold
`method`	Character vector, either ’glm’, ’glmer’ or ’bayesglm’
`check_logged`	Set FALSE to override sanity checks that try to ensure that the default assay is log-transformed and has at least one exact zero
`Silence`	Common problems with fitting some genes

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

A matrix of differentially expressed genes and related statistics.

MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data G Finak, A McDavid, M Yajima, J Deng, V Gersuk, AK Shalek, CK Slichter et al Genome biology 16 (1), 278

Coolgenome/iTALK documentation built on Aug. 3, 2019, 3:12 p.m.