loadConvergenceData: Load convergence information from RDS files

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

Description

Load convergence information from RDS files.

Usage

loadConvergenceData(analysisResultsDir, permutationResultsDir,
  type = c("sites", "tiles"), inter = c("i2", "iAll"), position,
  by = 100)

Arguments

analysisResultsDir	a character string, the path to the directory that contains the analysis results. The path can be the same as for the permutatioNResultsDir parameter.
permutationResultsDir	a character string, the path to the directory that contains the permutation results. The path can be the same as for the analysisResultsDir parameter.
type	One of the "sites" or "tiles" strings. Specifies the type of differentially methylated elements should be returned. For retrieving differentially methylated bases type = "sites"; for differentially methylated regions type = "tiles". Default: "sites".
inter	One of the "i2" or "iAll" strings. Specifies the type of intersection should be returned. For retrieving intersection results between two consecutive generations inter = "i2"; for intersection results between three generations or more inter = "iAll". Default: "i2".
position	a positive integer, the position in the list where the information will be extracted.
by	a integer, the increment of the number of permutations where the significant level is tested. Default: 100.

Value

a graph showing the evolution of the significant level with the number of permutations

Author(s)

Astrid Deschenes, Pascal Belleau

Examples

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

## Load convergence information
results <- loadConvergenceData(analysisResultsDir = filesDir,
    permutationResultsDir = filesDir, type="sites", inter="i2", position=1,
    by=1)

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