readExposome {rexposome} | R Documentation

## Creation of an ExposomeSet from files

### Description

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

### Usage

    readExposome(
      exposures,
      description,
      phenotype,
      sep = ",",
      na.strings = c("NA", "-", "?", " ", ""),
      exposures.samCol = "sample",
      description.expCol = "exposure",
      description.famCol = "family",
      phenotype.samCol = "sample",
      exposures.asFactor = 5,
      warnings = TRUE
    )

### Arguments

`exposures` | String with the path to the file with the matrix of exposures.
`description` | String with the path to the file with the description of the exposures (relation between exposures and exposure-family).
`phenotype` | String with the path to the file with the phenotypes of interest.
`sep` | (default `","`) Separator used by `read.table` to load the files "exposures", "description" and "phenotype".
`na.strings` | (default `c("NA", "-", "?", " ", "")`) Character defining the `NA` values in expsome's files.
`exposures.samCol` | (default `"sample"`) Index where the samples' name are found in file "exposures". It can be both charatcer or numeric.
`description.expCol` | (default `"exposure"`) Index where the exposures' name are found in file "description". It can be both numeric or character.
`description.famCol` | (default `"family"`) Index where the family's name (per exposures) if found in file "description". It can be both numeric or character.
`phenotype.samCol` | (default `"sample"`) Index where the sample's name are found in file "phenotype". 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 file, that corresponds to samples' names, must be the same than the phenotype's file. In the same way, the columns in exposure's file must be the same found as rows in description file.

### 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, loadExposome for constructor from loaded `data.frame`s

### Examples

    ## Locate the data-files
    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")

    ## Create ExposomeSet from files
    exp <- readExposome(
      exposures = exposures,
      description = description,
      phenotype = phenotype,
      exposures.samCol = 1,
      description.expCol = 2,
      description.famCol = 1,
      phenotype.samCol = 1
    )

[Package rexposome version 1.12.4 Index]