MARVEL (version 1.4.0)

IsoSwitch: 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(
  MarvelObject,
  method,
  psi.pval = 0.1,
  psi.delta = 0,
  gene.pval = 0.1,
  gene.log2fc = 0.5,
  event.type = NULL,
  custom.tran_ids = NULL
)

Value

An object of class S3 containing with new slots MarvelObject$DE$Cor$Table, MarvelObject$DE$Cor$Plot, and MarvelObject$DE$Cor$Plot.Stats.

Arguments

MarvelObject

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

method

Character string. The statistical method used for differential splicing analysis.

psi.pval

Numeric value. Adjusted p-value below which the splicing event is considered differentially spliced and included for isoform switching analysis. To be used in conjunction with psi.delta.

psi.delta

Numeric value. The absolute mininum difference in PSI values between the two cell groups above which the splicing event is considered differentially spliced nd included for isoform switching analysis. To be used in conjunction with psi.pval. Specify 0 (default) to switch this threshold off.

gene.pval

Numeric value. Adjusted p-value below which the gene is considered differentially expressed. Default value is 0.1.

gene.log2fc

Numeric value. The absolute log2 fold change in mean gene expression values between the two cell groups above which the gene is considered differentially expressed. To be used in conjunction with gene.pval. Specify 0 to switch this threshold off. Default value is 0.5.

event.type

Character string. Indicate which splicing event type to include for analysis. Can take any combination of values: "SE", "MXE", "RI", "A5SS", "A3SS", "AFE}, or \code{"ALE.

custom.tran_ids

Vector of character strings. Subset of tran_ids to be brought forward for analysis after filtering based on psi.pval and psi.delta.

Examples

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

marvel.demo <- IsoSwitch(MarvelObject=marvel.demo,
                         method="ad",
                         psi.pval=0.1,
                         psi.delta=0,
                         gene.pval=0.1,
                         gene.log2fc=0.5
                         )

# Check outputs
head(marvel.demo$DE$Cor$Table_Raw)
head(marvel.demo$DE$Cor$Table)
marvel.demo$DE$Cor$Plot
marvel.demo$DE$Cor$Plot.Stats