DysPIA: DysPIA: Dysregulated Pathway Identification Analysis

In DysPIA: Dysregulated Pathway Identification Analysis

Description

Runs Dysregulated Pathway Identification Analysis (DysPIA).The package 'DysPIAData' including the background data is needed to be loaded.

Usage

DysPIA(
  pathwayDB = "kegg",
  stats,
  nperm = 10000,
  minSize = 15,
  maxSize = 1000,
  nproc = 0,
  DyspiaParam = 1,
  BPPARAM = NULL
)

Arguments

pathwayDB	Name of the pathway database (8 databases:reactome,kegg,biocarta,panther,pathbank,nci,smpdb,pharmgkb). The default value is "kegg".
stats	Named vector of CILP scores for each gene pair. Names should be the same as in pathways.
nperm	Number of permutations to do. Minimial possible nominal p-value is about 1/nperm. The default value is 10000.
minSize	Minimal size of a gene pair set to test. All pathways below the threshold are excluded. The default value is 15.
maxSize	Maximal size of a gene pair set to test. All pathways above the threshold are excluded. The default value is 1000.
nproc	If not equal to zero sets BPPARAM to use nproc workers (default = 0).
DyspiaParam	DysPIA parameter value, all gene pair-level status are raised to the power of 'DyspiaParam' before calculation of DysPIA enrichment scores.
BPPARAM	Parallelization parameter used in bplapply. Can be used to specify cluster to run. If not initialized explicitly or by setting 'nproc' default value 'bpparam()' is used.

Value

A table with DysPIA results. Each row corresponds to a tested pathway. The columns are the following:

• pathway – name of the pathway as in 'names(pathway)';

• pval – an enrichment p-value;

• padj – a BH-adjusted p-value;

• DysPS – enrichment score, same as in Broad DysPIA implementation;

• NDysPS – enrichment score normalized to mean enrichment of random samples of the same size;

• nMoreExtreme' – a number of times a random gene pair set had a more extreme enrichment score value;

• size – size of the pathway after removing gene pairs not present in 'names(stats)';

• leadingEdge – vector with indexes of leading edge gene pairs that drive the enrichment.

Examples

data(pathway_list,package="DysPIAData")
data(DysGPS_p53)
DyspiaRes_p53 <- DysPIA("kegg", DysGPS_p53, nperm = 100, minSize = 20, maxSize = 100)

DysPIA documentation built on July 10, 2020, 9:06 a.m.