CompareValues.Genes.10x: Differential gene expression analysis

In wenweixiong/MARVEL: Revealing Splicing Dynamics at Single-Cell Resolution

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)

wenweixiong/MARVEL documentation built on Aug. 5, 2024, 2:54 p.m.