plotConvergenceGraph: Generate a graph showing the convergence for a permutation...

In methylInheritance: Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multiple Generations to a Treatment Effect

Description

Generate a graph showing the convergence for a permutation analysis using observed and permuted results.

Usage

plotConvergenceGraph(dataFrameConvergence)

Arguments

dataFrameConvergence

a data.frame containing the significant levels at different number of cycles (total number of permuted data analysed). The data.frame must have 6 columns : "NBR_PERMUTATIONS", "ELEMENT". "ANALYSIS", "POSITION", "TYPE" and "SIGNIFICANT_LEVEL". The "ELEMENT" can be either "SITES" or "TILES". The "TYPE" can be either "HYPER" or "HYPO".

Value

a ggplot object.

Author(s)

Astrid Deschenes, Pascal Belleau

Examples

## Get the name of the directory where files are stored
filesDir <- system.file("extdata", "TEST", package="methylInheritance")

## Extract convergenc information for F1 and F2 and F3
data <- loadConvergenceData(analysisResultsDir = filesDir,
    permutationResultsDir = filesDir, type = "sites", inter = "iAll",
    position = 1, by = 1)

## Create convergence graph
plotConvergenceGraph(data)

methylInheritance documentation built on Nov. 8, 2020, 8:21 p.m.