CompareValues.Exp.Spliced {MARVEL}

Differential gene expression analysis for differentially spliced genes

Description

Performs differential gene expression analysis between 2 groups of cells only on differentially spliced genes.

Usage

CompareValues.Exp.Spliced(
  MarvelObject,
  cell.group.g1 = NULL,
  cell.group.g2 = NULL,
  psi.method,
  psi.pval,
  psi.delta,
  method.de.gene = "wilcox",
  method.adjust.de.gene = "fdr",
  downsample = FALSE,
  seed = 1,
  show.progress = TRUE,
  mast.method = "bayesglm",
  mast.ebayes = TRUE
)

Arguments

MarvelObject

Marvel object. S3 object generated from TransformExpValues function.

cell.group.g1

Vector of character strings. Cell IDs corresponding to Group 1 (reference group).

cell.group.g2

Vector of character strings. Cell IDs corresponding to Group 2.

psi.method

Vector of character string(s). To include significant events from these method(s) for differential gene expression analysis.

psi.pval

Vector of numeric value(s). The adjusted p-value, below which, the splicing event is considered differentially spliced, and the corresponding genes will be included for differential gene expression analysis.

psi.delta

Numeric value. The absolute difference in mean PSI values between cell.group.g1 and cell.group.g1, above which, the splicing event is considered differentially spliced, and the corresponding genes will be included for differential gene expression analysis.

method.de.gene

Character string. Same as method in CompareValues function.

method.adjust.de.gene

Character string. Same as method in CompareValues function.

downsample

Logical value. If set to TRUE, the number of cells in each cell group will be downsampled to the sample size of the smaller cell group so that both cell groups will have the sample size prior to differential expression analysis. Default is FALSE.

seed

Numeric value. The seed number for the random number generator to ensure reproducibility during during down-sampling of cells when downsample set to TRUE.

show.progress

Logical value. If set to TRUE, progress bar will be displayed so that users can estimate the time needed for differential analysis. Default value is TRUE.

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 new slot MarvelObject$DE$Exp$Table.

Examples

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

# Define cell groups for analysis
df.pheno <- marvel.demo$SplicePheno
cell.group.g1 <- df.pheno[which(df.pheno$cell.type=="iPSC"), "sample.id"]
cell.group.g2 <- df.pheno[which(df.pheno$cell.type=="Endoderm"), "sample.id"]

# DE
marvel.demo <- CompareValues.Exp.Spliced(MarvelObject=marvel.demo,
                                         cell.group.g1=cell.group.g1,
                                         cell.group.g2=cell.group.g2,
                                         psi.method="ad",
                                         psi.pval=0.10,
                                         psi.delta=0,
                                         method.de.gene="t.test",
                                         method.adjust.de.gene="fdr",
                                         show.progress=FALSE
                                         )

# Check output
head(marvel.demo$DE$Exp.Spliced$Table)