crossomics {omicRexposome}R Documentation

Function to perform a Transcriptome-Wide Association Study

Description

This function allows to perform a Transcriptome-Wide Association Study by using an ExposmeSet and an ExpressionSet. It allows to perform an adjustment using Surrogate Variable Analysis (from R package sva).

Usage

crossomics(object, method = "mcca", ncomponents = 2, ..., na.rm = FALSE,
  permute = c(100, 3), verbose = FALSE, warnings = TRUE)

## S4 method for signature 'MultiDataSet'
crossomics(object, method = "mcca",
  ncomponents = 2, ..., na.rm = FALSE, permute = c(100, 3),
  verbose = FALSE, warnings = TRUE)

Arguments

object

A MultiDataSet object containing at last two data-sets like ExposomeSet, ExpressionSet, MethylationSet...

method

(default "mcca") It can takes values "mcca" for Multiple Canonical Correlation Analysis or "mcia" for Multiple Co-Inertia Analysis.

ncomponents

(default 2) Number of components to be estimated.

...

Other arguments given to mcia (from omicade4) or to MultiCCA (from PMA).

na.rm

(default FALSE) If method was set to "mcca" and na.rm was set to TRUE, features containing missing values are removed.

permute

(default c(100, 3)). If method="mcca" and this agument is set to NULL no permutation test to tune-up the parameters for MultiCCA. When filles, permute[1] corresponds to the number permutations (default in MultiCCa.permute is 25) and permute[2] the number of iterations (default in MultiCCA.permute is 3).

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)
library(rexposome)
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, imputation(brge_expo),
    dataset.type = "exposures", GRanges = NA)

crs <- crossomics(mds, method = "mcia")
crs
[Package omicRexposome version 1.0.1 Index]