BioPathways.10x {MARVEL}

Pathway enrichment analysis

Description

Performs pathway enrichment analysis on differentially spliced genes or user-specified custom set of genes.

Usage

BioPathways.10x(
  MarvelObject,
  pval = 0.05,
  log2fc = NULL,
  delta = 5,
  min.gene.norm = 0,
  method.adjust = "fdr",
  custom.genes = NULL,
  species = "human",
  remove.ribo = FALSE
)

Arguments

MarvelObject

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

pval

Numeric value. p-value, above which, the splice junction is considered differentially spliced. Default is 0.05.

log2fc

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 has been specified.

delta

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 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.

method.adjust

Character string. Adjust p-values for multiple testing. Options available as per p.adjust function.

custom.genes

Character strings. Alternative to pval and delta. Vector of gene names to be assessed for enrichment of biological pathways.

species

Character strings. Takes the value "human" or "mouse", which corresponds to human and mouse genes, respectively. Default value is "human".

remove.ribo

Logical value. If set to TRUE, ribosomal genes will be removed prior to GO analysis. This may prevent high-expressing ribosomal genes from overshadowing more biological relevant genes for GO analysis. Default value is FALSE.

method

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

Value

An object of class S3 containing new slot MarvelObject$DE$BioPathways$Table.

Examples

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

marvel.demo.10x <- BioPathways.10x(
                        MarvelObject=marvel.demo.10x,
                        custom.genes=c("TPM2", "GNAS"),
                        species="human"
                        )