association-methods: # —————— Method to perform an association study...

In omicRexposome: Exposome and omic data associatin and integration analysis

Description

This function allows to perform an association study between gene expression from microarray and the exposome. An ExpresionSet is the object storing the gene expresion and an ExposomeSet the one storing the exposome. Both of them needs to be encapsulated in a MultiDataSet. The association study is perform through standard limma pipeline. The function allows to perform multiple tests using the argument exposures.

Usage

association(object, formula, expset, omicset, set = "exposures",
  method = "ls", ..., baselevels, sva = "none", vfilter = NULL,
  verbose = FALSE, warnings = TRUE)

## S4 method for signature 'MultiDataSet'
association(object, formula, expset, omicset,
  set = "exposures", method = "ls", ..., baselevels, sva = "none",
  vfilter = NULL, verbose = FALSE, warnings = TRUE)

Arguments

object	A MultiDataSet object containing at last one omic data-sets like ExpressionSet, MethylationSet... and, at last, one ExposomeSet.
formula	formula to be evaluated by each exposure (or phenotype, see set argument). It should not contain any exposures (or phenotype), it will be added automatically when evaluated.
expset	Name of the ExposomeSet in object.
omicset	Name of the omic data-set in object.
set	(default "exposures") Can take value "exposures" to test the association of the exposures in the ExposomeSet vs. the features in the omic data-set. If takes "phenotypes" all phenotypes in ExposomeSet are tested.
method	(default "lm") Check limma help pages.
...	Arguments passed to limma's lmFit.
baselevels	(optional) If set, must be a labeled vector with the default base level for categorical exposures.
sva	(default "none"). This argument can take value "none" to do not apply SVA. Value "fast" will run SVA using isva and SmartSVA. Value "slow" will run SVA using sva.
vfilter	(default NULL). Only used when sva = "slow". Numeric number of probes used in sva. Recomended ~10% of real probes.
verbose	(default FALSE) If set to TRUE, a series of messages descriving the process are shown.
warnings	(default TRUE) If set to TRUE, a series of warnings are shown when required user atention.

Value

An object of class ResultSet.

Examples

library(MultiDataSet)
data(brge_prot, package = "brgedata")
data(brge_expo, package = "brgedata")
mds <- createMultiDataSet()
mds <- add_eset(mds, brge_prot, dataset.type = "proteines")
mds <- add_eset(mds, brge_expo, dataset.type = "exposures", GRanges = NA)

asr <- association(mds, formula = Asthma ~ Sex + Age,
  expset = "exposures", omicset = "proteines")
asr

omicRexposome documentation built on Jan. 24, 2021, 2:03 a.m.