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

In rexposome: Exposome exploration and outcome data analysis

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")

Example output

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Registered S3 method overwritten by 'pryr':
  method      from
  print.bytes Rcpp

Attaching package: ‘rexposome’

The following object is masked from ‘package:BiocGenerics’:

    plotPCA

Warning message:
In exwas(expo[1:5, ], asthma ~ 1, family = "binomial") :
  Data from 'asthma~lddt_lip+1' was reduced from 1200 to 1185
Warning message:
In exwas(expo[1:5, ], asthma ~ sex + age, family = "binomial") :
  Data from 'asthma~lddt_lip+sex + age' was reduced from 1200 to 1185
Warning message:
In exwas(expo[1:5, ], asthma ~ age, family = "binomial", filter = sex ==  :
  Data from 'asthma~lddt_lip+age' was reduced from 593 to 585

rexposome documentation built on March 13, 2021, 2:01 a.m.