Exposome exploration and outcome data analysis


[Up] [Top]

Documentation for package ‘rexposome’ version 1.29.0

Help Pages

C D E F G H I L M N P R S T V misc

-- C --

classification Method to get the classification of the samples from an ExposomeClust.
classification-method Class ExposomeClust
clustering Method to perform clustering on the samples of an ExposomeSet
clustering-method Class ExposomeSet
correlation Creation of an ExposomeCorr from an ExposomeSet.
correlation-method Class ExposomeSet

-- D --

dim-method Class ExposomeCorr
dim-method Class ExposomeSet
dim-method Class imExposomeSet

-- E --

expo 'ExposomeSet' for testing purpouses
expos Returns the exposures matrix of an ExposomeSet.
expos-method Class ExposomeSet
expos-method Class imExposomeSet
ExposomeClust Class ExposomeClust
ExposomeClust-class Class ExposomeClust
ExposomeCorr Class ExposomeCorr
ExposomeCorr-class Class ExposomeCorr
ExposomePCA Class ExposomePCA
ExposomePCA-class Class ExposomePCA
ExposomeSet Class ExposomeSet
ExposomeSet-class Class ExposomeSet
exposureNames Getter to obtain the exposures's names of an ExposomeSet or ExposomePCA
exposureNames-method Class ExposomePCA
exposureNames-method Class ExposomeSet
exposureNames-method Class imExposomeSet
expo_c 'ExposomeClust' for testing purpouses
extract Raw data from 'ExWAS', 'ExposomeClust' and 'ExposomeCorr'.
extract Raw data from 'ExWAS'
extract-method Class ExWAS
extract-method Class ExposomeCorr
extract-method Class ExposomePCA
extract-method Class imExposomeSet
extract-method Class mExWAS
ExWAS Class ExWAS
exwas Testing the association between an exposure and a phenotype of an ExposomeSet
ExWAS-class Class ExWAS
exwas-method Class ExposomeSet
exwas-method Class imExposomeSet
ex_imp 'imExposomeSet' for testing purpouses

-- F --

familyNames Getter to obtain the exposures's names of an ExposomeSet.
familyNames-method Class ExposomeSet
familyNames-method Class imExposomeSet

-- G --

get_robust_sd Raw data from 'ExWAS'
get_robust_sd-method Class ExWAS

-- H --

highAndLow Function to convert continuous exposures to categorical exposures
highAndLow-method Class ExposomeSet

-- I --

ilod Function to impute under-LOD values from an ExposomeSet
ilod-method Class ExposomeSet
imExposomeSet Class imExposomeSet
imExposomeSet-class Class imExposomeSet
imExposomeSet-methods Class imExposomeSet
imputation Function to impute missing values from an ExposomeSet
imputation-method Class ExposomeSet
imputeLOD Function to impute values under limit of detection
invExWAS Testing the association between an exposure and a phenotype of an ExposomeSet (modelling the exposures as response)
invExWAS-method Class ExposomeSet

-- L --

loadExposome Creation of an ExposomeSet from 'data.frames'
loadExposome_plain Creation of an ExposomeSet from single 'data.frame'
loadImputed Creation of an imExposomeSet from 'data.frames'

-- M --

me 'data.frame' for testing purpouses
mExWAS Class mExWAS
mexwas Testing the association between an exposure and a phenotype of an ExposomeSet using a multivariate aproach.
mExWAS-class Class mExWAS
mexwas-method Class ExposomeSet

-- N --

names-method Class ExWAS
ndim Number of principal components in an ExposomePCA.
ndim-method Class ExposomePCA
normalityTest It creates a 'data.frame' of boolean indicating if the exposures follows a normal distribution or not.
normalityTest-method Class ExposomeSet

-- P --

pca Creation of an ExposomePCA from an ExposomeSet.
pca-method Class ExposomeSet
phenotypeNames Getter to obtain the phenotype's names of an ExposomeSet or ExposomePCA.
phenotypeNames-method Class ExposomePCA
phenotypeNames-method Class ExposomeSet
phenotypeNames-method Class imExposomeSet
plot-method Class ExWAS
plot-method Class ExposomeClust
plot-method Class ExposomeCorr
plot-method Class ExposomePCA
plot-method Class ExposomeSet
plot-method Class imExposomeSet
plot-method Class mExWAS
plot3PCA Ploting PCA in a 3D space
plot3PCA-method Class ExposomePCA
plotClassification Draw the profile of the levels exposures after a classification with a clustering method
plotClassification-method Class ExposomeClust
plotCorrelation It draws both circos or matrix plot for the correlation in ExposomeCorr
plotCorrelation-method Class ExposomeCorr
plotEffect Function to draw a plot of the pvalues stored in an 'ExWAS' object
plotEffect-method Class ExWAS
plotEXP Plot correlation between exposures and PCA
plotEXP-method Class ExposomePCA
plotExwas Function to draw a plot of the pvalues stored in an 'ExWAS' object
plotExwas-method Class ExWAS
plotExwas-method Class mExWAS
plotFamily It draws the profile of the exposome in an ExposomeSet
plotFamily-method Class ExposomeSet
plotFamily-method Class imExposomeSet
plotHistogram It draws a histogram for each exposure in an ExposomeSet
plotHistogram-method Class ExposomeSet
plotLOD It draws a chart with the percentage of under-LOD values in an ExposomeSet
plotLOD-method Class ExposomeSet
plotMissings It draws a chart with the percentage of missing in an ExposomeSet
plotMissings-method Class ExposomeSet
plotPCA Ploting PCA
plotPCA-method Class ExposomePCA
plotPHE Plot association score between phentoypes and PCA
plotPHE-method Class ExposomePCA
plotVolcano Function to draw a plot of the pvalues stored in an 'ExWAS' object
plotVolcano-method Class ExWAS

-- R --

readExposome Creation of an ExposomeSet from files
rexposome rexposome: Package for exposome exploration and outcome data analysis

-- S --

sampleNames-method Class ExposomeClust
sampleNames-method Class imExposomeSet
standardize #' Summary of an ExposomeSet. #' #' Given an ExposomeSet is shows a summary for its exposures or #' its phenotypes. #' #' @name Summary #' @rdname Summary-methods #' @aliases Summary #' @param object codeExposomeSet with 'set' will be summarized. #' @param set Set to be sumarized ('"exposures"' or '"phenotypes"'). #' @param select Subseting of exposures of phenotypes. #' @return A basic description of the exposures in the 'ExposomeSet' #' @examples #' data("exposome") #' Summary(expo, set = "exposures") #' @export Summary setGeneric("Summary", function(object, set=c("exposures", "phenotypes"), select) standardGeneric("Summary") ) Standardize of an ExposomeSet.
standardize-method Class ExposomeSet
Summary-method Class ExposomeSet

-- T --

tableLOD It creates a vector with the amount of under-LOD exposures in an ExposomeSet
tableLOD-method Class ExposomeSet
tableMissings It creates a vector with the amount of missing in an ExposomeSet
tableMissings-method Class ExposomeSet
tef Function to get the Threshold for effective tests (TEF)
tef-method Class ExWAS
toES Method to convert an imExposomeSet to an ExposomeSet
toES-method Class imExposomeSet
trans Function to apply a transformation to the exposures of an ExposomeSet
trans-method Class ExposomeSet

-- V --

volcano_plot Function to draw a Volcano Plot

-- misc --

[ Class imExposomeSet
[-method Class imExposomeSet
[[-method Class imExposomeSet