extractEnrichment: Extract enrichment

In rtmag/forkedTF: Creation of Forked-Position Weight Matrices, a graph model of multiple PWMs.

Description

Extracts the information for genomic enrichment.

Usage

extractEnrichment(
  categories,
  tail,
  categoriesOverlaps,
  theoricalMeans,
  categoriesCount,
  pAdjust = "BH"
)

Arguments

tail	If "lower" then, probabilities are P[X > x], if "higher", P[X <= x], if "both" then higher or lower is selected depending on the number of overlaps vs the theorical mean.
categoriesOverlaps	The number of overlaps for each category.
theoricalMeans	The mean number of overlaps for each category.
categoriesCount	A vector representing the number of time a category is found in the catalog.
pAdjust	method used to correct p-values for multiple testing. Supported: "BH" (Benjamini-Hochberg), "BY", "bonferroni".
categories=unique(catalog@elementMetadata$id)	The categories contained in the catalog. This option is leaved for faster calculation when this function is runned multiple times.

Value

A data frame containing the enrichment informations.

Author(s)

Zacharie Menetrier

rtmag/forkedTF documentation built on Nov. 5, 2021, 10 a.m.