MonocleTest: Differential expression using monocle
In Coolgenome/iTALK: Characterize and Illustrate Intercellular Communication

Description Usage Arguments Details Value References

Identifies differentially expressed genes between two groups of cells using monocle

1 2	MonocleTest(sub_data, min_gene_expressed, min_valid_cells, contrast = unique(sub_data$compare_group), batch = NULL, cores = 4)

`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
`batch`	Different batch identifier
`cores`	The number of cores to be used while testing each gene for differential expression.

This test does not support pre-processed genes. To use this method, please install monocle, using the instructions at https://bioconductor.org/packages/release/bioc/html/monocle.html

A matrix of differentially expressed genes and related statistics.

Qiu X, Hill A, Packer J, Lin D, Ma Y, Trapnell C (2017). “Single-cell mRNA quantification and differential analysis with Census.” Nature Methods. https://github.com/cole-trapnell-lab/monocle-release

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