calculateSignificantLevel {methylInheritance}

R Documentation

Calculate significant level for hypo and hyper conserved elements

Description

Calculate significant level for hypo and hyper conserved elements using permutation results as well as observed results

Usage

calculateSignificantLevel(formatForGraphDataFrame)

Arguments

formatForGraphDataFrame

a data.frame containing the observation results (using real data) and the permutation results (using shuffled data). Both hyper and hypo differentially conserved methylation results must be present. The data.frame must have 3 columns : "TYPE", "RESULT" and "SOURCE". The "TYPE" can be either "HYPER" or "HYPO". The "RESULT" is the number of conserved differentially elements. The "SOURCE" can be either "OBSERVATION" or "PERMUTATION".

Value

a list containing two elements:

• HYPER a double, the significant level for the hyper differentially methylated conserved elements

• HYPO a double, the significant level for the hypo differentially methylated conserved elements

Author(s)

Astrid Deschenes, Pascal Belleau

Examples

## Loading dataset containing all results
data(methylInheritanceResults)

## Extract information for the intersection between conserved differentially
## methylated sites (type = sites) between the intersection of 2
## generations (inter = i2): F2 and F3 (position = 2)
info <- extractInfo(allResults = methylInheritanceResults,
    type = "sites", inter="i2", 2)

## Create graph
methylInheritance:::calculateSignificantLevel(info)

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