runRDA: Calculate RDA for a set

In isglobal-brge/MEAL: Perform methylation analysis and facilitates differential expression analyses

Description

Perform RDA calculation for a AnalysisRegionResults. Feature values will be considered the matrix X and phenotypes the matrix Y. Adjusting for covariates is done using a model matrix passed in covarsmodel.

Usage

runRDA(
  set,
  model,
  num_vars = ncol(model),
  range,
  betas = FALSE,
  resultSet = TRUE,
  num_permutations = 10000,
  ...
)

Arguments

set	MethylationSet, ExpressionSet or matrix
model	Model matrix or formula to get model matrix from set.
num_vars	Numeric with the number of variables in the matrix for which the analysis will be performed. Compulsory if equation is not null.
range	GenomicRanges with the region used for RDA
betas	If set is a GenomicRatioSet, should beta values be used? (Default: TRUE)
resultSet	Should results be encapsulated in a resultSet? (Default: TRUE)
num_permutations	Numeric with the number of permutations run to compute the p-value. (Default: 1e4)
...	Further arguments passed to rda.

Value

Object of class rda or resultSet

See Also

rda

Examples

if (require(minfiData)){
set <- ratioConvert(mapToGenome(MsetEx[1:10,]))
model <- model.matrix(~set$age)
rda <- runRDA(set, model)
rda
}

isglobal-brge/MEAL documentation built on May 8, 2021, 8:05 p.m.