Construct: Function for associating DNA methylation with matched mRNA...

In iloveless1/methylXprs: Associates DNA Methylation with Matched gene Expression

Description

This function allows you to associate DNA methylation with matched mRNA expression. There are three methods to choose from: 'Adjusted' in which one can adjust for race, 'Interaction' in which one can enforce a weak hierarchy and include race interaction terms, and 'Specific' in which one can associate in a race-specific manner.

Usage

Construct(
  Object = Object,
  method = c("Adjusted", "Interaction", "Specific"),
  dist = NULL,
  nfolds = NULL,
  impute = TRUE,
  beta = TRUE,
  parallel = FALSE,
  Methylation.Annotation = NULL,
  Gene.Annotation = NULL
)

Arguments

Object	an object of class Summarized Experiment containing paired DNA methylation, RNA seq, and Clinical data.
method	method for multivariate associations
dist	the distance from the TSS & TES in Kb. Defaults to 1,000,000Kb
nfolds	the number of folds to use for cross-validation
impute	Whether or not to impute the data. Defaults to TRUE
beta	Whether methylation matrix is beta-values, defaults to TRUE
parallel	whether to run in parallel. Defaults to FALSE
Methylation.Annotation	A Granges object annotating the methylation array used
Gene.Annotation	A GRanges object containing gene annotation.

Value

Large list with up to 5 columns

Examples

data('Testdat',package = 'EpiXprS')
Methy <- assays(Testdat)$Methyl450k
Methy[1:5,1:5]
Counts <- assays(Testdat)$RNASeqGene
Counts[1:2,1:5]
coldat <- colData(Testdat)
coldat$race <- ifelse(coldat$race == 'white',1,0)
head(coldat)
Construct(x = Methy, y = Counts, clinical = coldat$race,
method ='Interaction', dist = NULL, nfolds = NULL, 
impute = TRUE, beta = TRUE, parallel = FALSE,
Methylation.Annotation = annotation_450k, Gene.Annotation = annotated_RNA)

iloveless1/methylXprs documentation built on Dec. 20, 2021, 6:56 p.m.