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Differential expression using MAST

Source: R/DEG.R
MASTTest.Rd

Identifies differentially expressed genes between two groups of cells using MAST

Usage

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

Arguments

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'

silent

Common problems with fitting some genes

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

Value

A matrix of differentially expressed genes and related statistics.

Details

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

References

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