BioPathways {MARVEL}

Pathway enrichment analysis

Description

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

Usage

BioPathways(
  MarvelObject,
  method = NULL,
  pval = NULL,
  delta = 0,
  n.top = NULL,
  method.adjust = "fdr",
  custom.genes = NULL,
  species = "human"
)

Arguments

MarvelObject

Marvel object. S3 object generated from CompareValues function.

method

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

pval

Numeric value. Alternative to n.top and custom.genes, i.e. choose one of these three options. Adjusted p-value below which the splicing events are considered differentially spliced and their corresponding genes are included for gene ontology analysis. If this argument is specified, then n.top must not be specified.

delta

Numeric value. The absolute difference between the means PSI values of cell group 1 and 2, above which, the splicing event is considered differentially spliced and their corresponding genes are included for gene ontology analysis.

n.top

Numeric value. Alternative to pval to custom.genes, i.e. choose one of these three options.. Indicate the top n splicing events with the smallest adjusted p-values are differentially spliced and their corresponding genes are included for gene ontology analysis. If this argument is specified, then pval must not be specified.

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 n.top, i.e. choose one of these three options.. 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". This will enable MARVEL to retrieve the relevant database for GO analysis.

Value

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

Examples

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

marvel.demo <- BioPathways(MarvelObject=marvel.demo,
                           method="ad",
                           custom.genes=c("RPL26", "SNRPN")
                           )