CompareValues.Genes.10x {MARVEL}

Differential gene expression analysis

Description

Performs differential gene expression analysis between two groups of cells. Only among cells and genes previously included for splice junction analysis.

Usage

CompareValues.Genes.10x(
  MarvelObject,
  log2.transform = TRUE,
  show.progress = TRUE,
  method = "wilcox",
  mast.method = "bayesglm",
  mast.ebayes = TRUE
)

Arguments

MarvelObject

Marvel object. S3 object generated from CompareValues.SJ.10x function.

log2.transform

Logical value. If set to TRUE (default), normalised gene expression values will be off-set by 1 and then log2-transformed prior to analysis. This option is automatically set to TRUE if method option is set to "mast".

show.progress

Logical value. If set to TRUE (default), the progress bar will appear.

method

Character string. Statistical test to compare the 2 groups of cells. Default is "wilcox" as recommended by Seurat. Another option is "mast". If "mast" is specified, the log2fc and p-values will be corrected using the gene detection rate as per the MAST package tutorial.

mast.method

Character string. As per the method option of the zlm function from the MAST package. Default is "bayesglm", other options are "glm" and "glmer".

mast.ebayes

Logical value. As per the ebayes option of the zlm function from the MAST package. Default is TRUE.

Value

An object of class S3 with a updated slot MarvelObject$DE$SJ$Table.

Examples

marvel.demo.10x <- readRDS(system.file("extdata/data",
                               "marvel.demo.10x.rds",
                               package="MARVEL")
                               )

marvel.demo.10x <- CompareValues.Genes.10x(
                        MarvelObject=marvel.demo.10x,
                        show.progress=FALSE
                        )

# Check output
head(marvel.demo.10x$DE$SJ$Table)