loadExposome_plain: Creation of an ExposomeSet from single 'data.frame'

In isglobal-brge/rexposome: Exposome exploration and outcome data analysis

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"))

isglobal-brge/rexposome documentation built on Feb. 4, 2023, 12:35 p.m.