association {omicRexposome} | R Documentation

## # —————————————————————————– Method to perform an association study between transcriptome and exposom

### 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

[Package omicRexposome version 1.9.0 Index]