DysPIA (version 1.3)

calcDyspiaStat: calcDyspiaStat: Calculates DysPIA statistics

Description

Calculates DysPIA statistics for a given query gene pair set.

Usage

calcDyspiaStat(
  stats,
  selectedStats,
  DyspiaParam = 1,
  returnAllExtremes = FALSE,
  returnLeadingEdge = FALSE
)

Arguments

stats

Named numeric vector with gene pair-level statistics sorted in decreasing order (order is not checked).

selectedStats

Indexes of selected gene pairs in the `stats` array.

DyspiaParam

DysPIA weight parameter (0 is unweighted, suggested value is 1).

returnAllExtremes

If TRUE return not only the most extreme point, but all of them. Can be used for enrichment plot.

returnLeadingEdge

If TRUE return also leading edge gene pairs.

Value

Value of DysPIA statistic if both returnAllExtremes and returnLeadingEdge are FALSE. Otherwise returns list with the folowing elements:

• res -- value of DysPIA statistic

• tops -- vector of top peak values of cumulative enrichment statistic for each gene pair;

• bottoms -- vector of bottom peak values of cumulative enrichment statistic for each gene pair;

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