MARVEL (version 1.4.0)

IsoSwitch.10x: Classify gene-splicing relationship

Description

Classify gene-splicing relative changes to each other from cell group 1 to group 2. Classifications are coordinated, opposing, isoform-switching, and complex. In coordinated relationship, both gene and splicing changes in the same direction from cell group 1 to group 2. In opposing relationship, gene changes in the opposite direction relative to splicing from cell group 1 to group 2. In isoform-switching, there is differential splice junction usage without differential expression of the corresponding gene between cell group 1 and group 2. Complex relationship involves genes with both coordinated and opposing relationships with splicing. Only differentially spliced junctions are included for analysis here.

Usage

IsoSwitch.10x(
  MarvelObject,
  pval.sj = 0.05,
  log2fc.sj = NULL,
  delta.sj = 5,
  min.gene.norm = 0,
  pval.adj.gene = 0.05,
  log2fc.gene = 0.5
)

Value

An object of class S3 containing new slots MarvelObject$SJ.Gene.Cor$Data, MarvelObject$SJ.Gene.Cor$Proportion$Plot, and MarvelObject$SJ.Gene.Cor$Proportion$Table.

Arguments

MarvelObject

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

pval.sj

Numeric value. p-value from differential splicing analysis, below which, the splice junction is considered differentially spliced. Default is 0.05.

log2fc.sj

Numeric value. Absolute log2 fold change from differential splicing analysis, above which, the splice junction is considered differentially spliced. This option should be NULL if delta.sj has been specified.

delta.sj

Numeric value. Absolute difference in average PSI values between the two cell groups, above which, the splice junction is considered differentially spliced. This option should be NULL if log2fc.sj has been specified.

min.gene.norm

Numeric value. The average normalised gene expression across the two cell groups above which the splice junction is considered differentially spliced. Default is 0.

pval.adj.gene

Numeric value. Adjusted p-value from differential gene expression analysis, below which, the gene is considered differentially expressed. Default is 0.05.

log2fc.gene

Numeric value. Absolute log2 fold change from differential gene expression analysis, above which, the gene is considered differentially expressed. This option should be NULL if delta.sj has been specified.

Examples

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

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

marvel.demo.10x <- IsoSwitch.10x(
                        MarvelObject=marvel.demo.10x,
                        pval.sj=0.05,
                        delta.sj=5,
                        min.gene.norm=1.0,
                        pval.adj.gene=0.05,
                        log2fc.gene=0.5
                        )

# Check outputs
marvel.demo.10x$SJ.Gene.Cor$Proportion$Plot
marvel.demo.10x$SJ.Gene.Cor$Proportion$Table
cols <- c("coord.intron", "gene_short_name", "cor.complete")
head(marvel.demo.10x$SJ.Gene.Cor$Data[,cols])