runRDA: Calculate RDA for a set

Description Usage Arguments Value See Also Examples

View source: R/runRDA.R

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

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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)

Value

Object of class rda or resultSet

See Also

rda

Examples

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

MEAL documentation built on Nov. 1, 2018, 5:01 a.m.