DysPIA {DysPIA}

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)