DyspiaSimpleImpl {DysPIA}

DyspiaSimpleImpl

Description

Runs dysregulated pathway identification analysis for preprocessed input data.

Usage

DyspiaSimpleImpl(
  pathwayScores,
  pathwaysSizes,
  pathwaysFiltered,
  leadingEdges,
  permPerProc,
  seeds,
  toKeepLength,
  stats,
  BPPARAM
)

Arguments

pathwayScores

Vector with enrichment scores for the pathways in the database.

pathwaysSizes

Vector of pathway sizes.

pathwaysFiltered

Filtered pathways.

leadingEdges

Leading edge gene pairs.

permPerProc

Parallelization parameter for permutations.

seeds

Seed vector

toKeepLength

Number of 'pathways' that meet the condition for 'minSize' and 'maxSize'.

stats

Named vector of gene pair-level scores. Names should be the same as in pathways of 'pathwayDB'.

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.