loadExposome_plain {rexposome} | R Documentation

## Creation of an ExposomeSet from single `data.frame`

### Description

Creation of an ExposomeSet from single `data.frame`

### Usage

    loadExposome_plain(
      data,
      data_id,
      sep = ",",
      pheno_cols,
      na.strings = c("NA", "-", "?", " ", ""),
      families = NULL,
      exposures.asFactor = 5,
      warnings = TRUE
    )

### Arguments

`data` | `data.frame` With the exposures and phenotypes (in no particular order!) or `string` with the path to a file (.csv, .tsv, .txt) with the table of exposures and phenotypes
`data_id` | `character` Name of the column on the selected table that contains the ID
`sep` | `character` (default `","`) Separator used by `read.table` to load the files "exposures", "description" and "phenotype". Only applies when providing a path on the data argument
`pheno_cols` | `character` Character vector of the phenotype columns (all the other columns are considered exposures)
`na.strings` | `character` (default `c("NA", "-", "?", " ", "")`) Character defining the `NA` values in expsome's files.
`families` | `list` (default `NULL`) List to specify the families of the exposures, construct it as: `list(Family1 = c("exposure_1_1", "exposure_1_2", "exposure_1_n"), Family2 = c("exposure_2_1", "exposure_2_2", "exposure_2_n"), FamilyM = c("exposure_M_1", "exposure_M_2", "exposure_M_n"))`. All the exposures on the data table have to be on this provided list with their respective families. The family classification is optional, input `NULL` to bypass the family classifier
`exposures.asFactor` | `numeric` (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.

### Value

An object of class ExposomeSet.

### Examples

    path <- file.path(path.package("rexposome"), "extdata")
    phenotype <- file.path(path, "phenotypes.csv")
    exposures <- file.path(path, "exposures.csv")
    ee <- read.csv(exposures, header=TRUE)
    pp <- read.csv(phenotype, header=TRUE)
    # Create fake dataset with exposures and phenotypes combined
    data <- cbind(ee, pp)

    loadExposome_plain <- function(data, data_id = "idnum",
    pheno_cols = c("rhinitis", "wheezing", "sex", "age", "cbmi", "blood_pre", "whistling_chest","flu"))

[Package rexposome version 1.14.1 Index]