exwas-methods: Testing the association between an exposure and a phenotype...

In isglobal-brge/rexposome: Exposome exploration and outcome data analysis

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,
  robust = FALSE
)

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")

isglobal-brge/rexposome documentation built on Feb. 4, 2023, 12:35 p.m.