exwas {rexposome} | R Documentation

## Testing the association between an exposure and a phenotype of an ExposomeSet

### Description

The `exwas` method performs an "Exposome-Wide Association Study" (ExWAS) using the exposures in ExposomeSet and one of its phenotype.

### Usage

    exwas(
      object,
      formula,
      filter,
      family,
      ...,
      baselevels,
      tef = TRUE,
      verbose = FALSE,
      warnings = TRUE
    )

### Arguments

`object` | `ExposomeSet` that will be used for the ExWAS.
`formula` | `formula` indicating the test to be done. If any exposure is included it will be used as covariate. `exwas` metho will perform the test for each exposure.
`filter` | `expression` to be used to filter the individuals included into the test.
`family` | Family of the distribution followed by the health outcome to be tested (gaussian, bionomal, ... check glm).
`...` | NOT USED
`baselevels` | (optional) If set, must be a labeled vector with the default base level for categorical exposures.
`tef` | (default `TRUE`) If `TRUE` it computed the effective number of tests and the threhold for the effective number of tests. Usually it needs imputed data.
`verbose` | (default `FALSE`) If set o true messages along the tests are shown.
`warnings` | (default `TRUE`) If set to `FALSE` warnings will not be displayed.

### Value

An codeExWAS object with the result of the association study

### References

An Environment-Wide Association Study (ExWAS) on Type 2 Diabetes Mellitus. Chirag J. Patel, Jayanta Bhattacharya, Atul J. Butte. May 20, 2010 Plos One

Evaluating the effective numbers of independent tests and significant p-value thresholds in commercial genotyping arrays and public imputation reference datasets. Miao-Xin Li, Juilian M. Y. Yeung, Stacey S. Cherny and Pak C. Sham. May 2012 Hum Genet.

### See Also

extract to obtain a table with the result of the ExWAS, plotExwas to plot the results of the ExWAS

### Examples

    data(exposome)
    w1 <- exwas(expo[1:5, ], asthma~1, family = "binomial")
    w2 <- exwas(expo[1:5, ], asthma~sex+age, family = "binomial")
    w3 <- exwas(expo[1:5, ], asthma~age, family = "binomial", filter = sex=="boy")

[Package rexposome version 1.14.1 Index]