ExWAS {rexposome} | R Documentation

## Class ExWAS

### Description

Class `ExWAS` obtained from exwas method of an ExposomeSet object, contains the result of testing the association of exposures of an `ExposomeSet` to its phenotypes. "ExWAS" is the acronym of "Exposome-Wide Association Study". The function can be applied to one of to many phenotypes in the `ExposomeSet` object.

### Usage

    ## S4 method for signature 'ExWAS,ANY'
    plot(x, y, ...)

    ## S4 method for signature 'ExWAS'
    extract(object, sort = TRUE, ...)

    ## S4 method for signature 'ExWAS'
    names(x)

    ## S4 method for signature 'ExWAS'
    plotEffect(x, y, select, labels, xlab, ylab)

    ## S4 method for signature 'ExWAS'
    plotExwas(
      object,
      ...,
      subtitles,
      color,
      exp.order,
      labels,
      show.effective = TRUE
    )

    ## S4 method for signature 'ExWAS'
    plotVolcano(x, p.value = -log10(0.001), labels, show.effect = FALSE)

    ## S4 method for signature 'ExWAS'
    tef(object)

### Arguments

`x` | An `ExWAS` object
`y` | An `ExWAS` object
`...` | NOT USED
`object` | An object of class `ExWAS`, `mExWAS` or `nlExWAS`.
`sort` | If `TRUE`, the results are ordered by pvalue.
`select` | (optional) Vector with the selected exposures
`labels` | (optional) Character vector with the labels for each exposure. It must be labeled vector.
`xlab` | (optional) Label for x-axis
`ylab` | (optional) Label for y-axis
`subtitles` | Character vector with the "subtitle" for each plot when given more than one `ExWAS`.
`color` | (optional) A vector of colors. The vector must have length equal to the number of families. The vector must be names with the name of the families.
`exp.order` | (optional) Order of the exposures.
`show.effective` | (default TRUE) draws a brown line on the threshold given by the effective number of tests.
`p.value` | (default `-log10(0.001)`) Is the threshold from where the exposures can be taken as significants.
`show.effect` | (default `false`) Apply `exp` to obtained beta.

### Value

An object of class `ExWAS`

### Methods (by generic)

- `plot`: Wrapper for `plotExwas` method.

- `extract`: Method to obtain the matrix of association scores

- `names`: Method to obtain the Threshold for effective tests (TEF)

- `plotEffect`: Draws a plot with the confidence interval of each exposure. Alows to compare two ExWAS instances.

- `plotExwas`: Method to plot a manhatan plot for association between exposures and phenitypes

- `plotVolcano`: Method to plot a volcano plot for association between exposures and phenotypes

- `tef`: Method to obtain the Threshold for effective tests (TEF)

### Slots

`effective`

  Number containing the effective number of tests.

`formula`

  Tested formula.

`comparison`

  Result of performing the test to find association between levels of exposures and phenotype.

`description`

  Description of the exposures used in the ExWAS. (in description file).

### See Also

`exwas` to perform an Exposome-Wide Association Study and to create an `ExWAS`, `mexwas` to perform a Multivariate Exposome-Wide Association Study and to create a `mExWAS`

[Package rexposome version 1.12.4 Index]