loadAllRDSResults: Load all RDS files created by the permutation and observation...

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

Description

Load all RDS files created by the permutation and observation analysis. The function returns an object of class "methylInheritanceAllResults" that holds all the pertinent information.

Usage

loadAllRDSResults(
  analysisResultsDir,
  permutationResultsDir,
  doingSites = TRUE,
  doingTiles = FALSE,
  maxID = NA
)

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. When NULL, the observation results are not loaded. Default = NULL.
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. When NULL, the permutation results are not loaded. Default = NULL.
doingSites	a logical, the data related to differentially methylated sites are loaded when doingSites = TRUE. Default: TRUE.
doingTiles	a logical, the data related to differentially methylated tiles are loaded when doingTiles = TRUE. Default: TRUE.
maxID	NA or a positive integer, the maximum identification number of the permutation files to be loaded. When NA, all files present in the directory are loaded. Default: NA.

Value

a list of class methylInheritanceAllResults containing the result of the observation analysis as well as the results of all the permutations.

Author(s)

Astrid Deschenes, Pascal Belleau

See Also

mergePermutationAndObservation for detail description, in the Value section, of the methylInheritanceAllResults object.

Examples

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

## Load information from files
results <- loadAllRDSResults(analysisResultsDir = filesDir,
    permutationResultsDir = filesDir, doingSites = TRUE, doingTiles = TRUE)

## Print the observation results
results

## Access the results for the first permutation only for sites
results$PERMUTATION[[1]]$SITES

adeschen/methylInheritance documentation built on April 21, 2021, 9:45 a.m.