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Differential expression using DEsingle

Source: R/DEG.R
DESingleTest.Rd

Identifies differentially expressed genes between two groups of cells using DEsingle

Usage

DESingleTest(
  sub_data,
  min_gene_expressed,
  min_valid_cells,
  contrast = unique(sub_data$compare_group),
  parallel = FALSE,
  BPPARAM = bpparam()
)

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

parallel

If FALSE (default), no parallel computation is used; if TRUE, parallel computation using BiocParallel, with argument BPPARAM.

BPPARAM

An optional parameter object passed internally to bplapply when parallel=TRUE. If not specified, bpparam() (default) will be used.

Value

A matrix of differentially expressed genes and related statistics.

Details

This test does not support pre-processed genes. To use this method, please install DEsingle, using the instructions at https://github.com/miaozhun/DEsingle

References

Zhun Miao, Ke Deng, Xiaowo Wang, Xuegong Zhang (2018). DEsingle for detecting three types of differential expression in single-cell RNA-seq data. Bioinformatics, bty332. 10.1093/bioinformatics/bty332.