loadExposome {rexposome} | R Documentation

## Creation of an ExposomeSet from `data.frames`

### Description

Given three `data.frames` that defines the exposome (measures of exposome, exposome description and individuals phentype) it loads them and creates an object of type ExposomeSet.

### Usage

    loadExposome(
      exposures,
      description,
      phenotype,
      description.famCol = "family",
      exposures.asFactor = 5,
      warnings = TRUE
    )

### Arguments

`exposures` | `data.frame` of exposures.
`description` | `data.frame` with the description of the exposures (relation between exposures and exposure-family).
`phenotype` | `data.frame` with the phenotypes of interest.
`description.famCol` | (default `"family"`) Index where the family's name (per exposures) if found in file "description". It can be both numeric or character.
`exposures.asFactor` | (default `5`) The exposures with more than this number of unique items will be considered as "continuous" while the exposures with less or equal number of items will be considered as "factor".
`warnings` | (default `TRUE`) If `TRUE` shows useful information/warnings from the process of loading the exposome.

### Details

The rows of the exposure's `data.frames`, that corresponds to samples' names, must be the same than the phenotype's `data.frames`. In the same way, the columns in exposure's `data.frames` must be the same in description `data.frame`.

### Value

An object of class ExposomeSet.

### Note

ExposomeSet's `fData` will contain some inner columns called `.std`, `.trn`, `.fct` and `.type` in order to trace the transformations an exposure suffers and to know, at eny moment, if an exposure is categorical or continuous. The "description" file can contains a column called `type` with values `"factor"` and `"numeric"` to speficy how an exposure needs to be understood. If given, this column will be renamed to `.type`. If not given, it will be created using `exposures.asFactor` value.

### See Also

ExposomeSet for class description, readExposome for constructor from txt/csv files.

### Examples

    path <- file.path(path.package("rexposome"), "extdata")
    description <- file.path(path, "description.csv")
    phenotype <- file.path(path, "phenotypes.csv")
    exposures <- file.path(path, "exposures.csv")
    dd <- read.csv(description, header=TRUE)
    ee <- read.csv(exposures, header=TRUE)
    pp <- read.csv(phenotype, header=TRUE)
    rownames(dd) <- dd[, 2]
    dd <- dd[ , -2]
    rownames(ee) <- ee[ , 1]
    ee <- ee[ , -1]
    rownames(pp) <- pp[ , 1]
    pp <- pp[ , -1]
    exp <- loadExposome(
    exposures = ee,
    description = dd,
    phenotype = pp,
    description.famCol = "Family"
    )

[Package rexposome version 1.16.0 Index]