C D E F G H I L M N P R S T V misc
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 |
dim-method | Class ExposomeCorr |
dim-method | Class ExposomeSet |
dim-method | Class imExposomeSet |
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 |
familyNames | Getter to obtain the exposures's names of an ExposomeSet. |
familyNames-method | Class ExposomeSet |
familyNames-method | Class imExposomeSet |
get_robust_sd | Raw data from 'ExWAS' |
get_robust_sd-method | Class ExWAS |
highAndLow | Function to convert continuous exposures to categorical exposures |
highAndLow-method | Class ExposomeSet |
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 |
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' |
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 |
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 |
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 |
readExposome | Creation of an ExposomeSet from files |
rexposome | rexposome: Package for exposome exploration and outcome data analysis |
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 |
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 |
volcano_plot | Function to draw a Volcano Plot |
[ | Class imExposomeSet |
[-method | Class imExposomeSet |
[[-method | Class imExposomeSet |