Description Usage Arguments Value Methods (by generic) Slots See Also
Class ExposomeSet
contains the exposure levels, the exposure's
description and the samples phenotype. It is the starting object for
rexposome
package and extends eSet.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117  ## S4 method for signature 'ExposomeSet,ANY'
plot(x, y, ...)
## S4 method for signature 'ExposomeSet'
clustering(object, method, cmethod, ..., warnings = TRUE)
## S4 method for signature 'ExposomeSet'
correlation(object, ..., warnings = TRUE)
## S4 method for signature 'ExposomeSet'
dim(x)
## S4 method for signature 'ExposomeSet'
expos(object)
## S4 method for signature 'ExposomeSet'
exposureNames(object)
## S4 method for signature 'ExposomeSet'
exwas(
object,
formula,
filter,
family,
...,
baselevels,
tef = TRUE,
verbose = FALSE,
warnings = TRUE
)
## S4 method for signature 'ExposomeSet'
familyNames(object, by.exposure = FALSE)
## S4 method for signature 'ExposomeSet'
highAndLow(
object,
ngroups = 3,
intervals = c("standard", "extreme"),
select,
drop = FALSE,
warnings = TRUE
)
## S4 method for signature 'ExposomeSet'
ilod(
object,
seed = 1234,
lod.col = "LOD",
pNA = 0.2,
tLog = FALSE,
method = "QRILC",
warnings = TRUE,
...
)
## S4 method for signature 'ExposomeSet'
imputation(object, select, ..., messages = FALSE)
## S4 method for signature 'ExposomeSet'
invExWAS(object, formula, filter, tef = TRUE, verbose = FALSE, warnings = TRUE)
## S4 method for signature 'ExposomeSet'
mexwas(object, phenotype, family, warnings = TRUE)
## S4 method for signature 'ExposomeSet'
normalityTest(
object,
exposure,
th = 0.05,
min.val = 5,
na.rm = TRUE,
warnings = TRUE
)
## S4 method for signature 'ExposomeSet'
pca(object, npc = 10, pca = FALSE, ...)
## S4 method for signature 'ExposomeSet'
phenotypeNames(object)
## S4 method for signature 'ExposomeSet'
plotFamily(x, family, group, group2, scatter = TRUE, na.omit = TRUE)
## S4 method for signature 'ExposomeSet'
plotHistogram(x, select, density = TRUE, show.trans = FALSE)
## S4 method for signature 'ExposomeSet'
plotLOD(object, lod.col = "LOD", x.max = 100, sort = TRUE)
## S4 method for signature 'ExposomeSet'
plotMissings(
object,
set = c("exposures", "phenotypes"),
x.max = 100,
sort = TRUE
)
## S4 method for signature 'ExposomeSet'
standardize(object, select, method = "normal", na.rm = TRUE, warnings = TRUE)
## S4 method for signature 'ExposomeSet'
Summary(x, set = c("exposures", "phenotypes"), select, ..., na.rm = FALSE)
## S4 method for signature 'ExposomeSet'
tableLOD(object, output = "n", lod.col = "LOD", sort = TRUE)
## S4 method for signature 'ExposomeSet'
tableMissings(
object,
set = c("exposures", "phenotypes"),
output = "n",
sort = TRUE
)
## S4 method for signature 'ExposomeSet'
trans(object, fun, select, by.exposure = FALSE, ...)

x 
An 
y 
NOT USED 
... 
Arguments to be passed to imputeFAMD 
object 
An 
method 
Method to be used. 
cmethod 
Function implementing a systsme to retrieve classification from clustering output 
warnings 
If set to 
formula 
Formula, not including exposures, to be tested. No need to provide response (left term) 
filter 
Expression to be used to filter 
family 
Family descriving the nature of the health outcome 
baselevels 
Labeled vector with the default base level for categorical exposures. 
tef 
If 
verbose 
If set to 
by.exposure 
If set to 
ngroups 
Number of intervals to be used 
intervals 
If 
select 
Vector selecting thee xposures to be used. 
drop 
If set to 
seed 
Numeric seed 
lod.col 
Indicator of the column where the LOD is located 
pNA 
Maximum percentage allowed of values under LOD 
tLog 
If set to 
messages 
If set to 
phenotype 
Health outcome to be used as dependent variable. 
exposure 
Vecror of exposures to be used. 
th 
Threshold of PValue used to considere normalit 
min.val 
Minimum number of observations to perform test 
na.rm 
If set to 
npc 
Number of PC to be kept 
pca 
Perform PCA (only numerical variables) or FAMD (numerical and categorical) 
group 
Phenotype to group exposures 
group2 
Phenotype to group exposures 
scatter 
If set to true it shows the samples value in the plot 
na.omit 
If set to 
density 
If set to 
show.trans 
If set to 
x.max 
Threshold for x axis (in %) 
sort 
If set to 
set 
Cantake values 
output 
Can take values 
fun 
Function to bt used in the transformation process 
An object of class ExposomeSet
plot
: Wrapper for plotFamily
method.
clustering
: Performs clustering on samples based on exposure levels.
correlation
: Computes correlation on exposures.
dim
: Returns the number of exsures, samples and phenotypes.
expos
: Returns a data.frame
with exposures.
exposureNames
: Getter to obtain the exposures's names.
exwas
: Performs an EXposomeWide Association Study
familyNames
: Getter to obtain the families's names of the
family of each exposure.
highAndLow
: Performs a discretization of continuous exposures.
ilod
: Imputation of underLOD values of exposures.
imputation
: Imputation of missing values of exposures.
invExWAS
: Performs an EXposomeWide Association Study (modelling the exposures as response)
mexwas
: Performs a MultipleEXposureWide Association Study.
normalityTest
: Test the normality of each exposure.
pca
: Performs a PCA
phenotypeNames
: Getter to obtain the phenotypes's names.
plotFamily
: Draws a boxplot or accumulatedbar plot for each
exposure in a given family.
plotHistogram
: Draws an histogram of a given continuous exposure
or a pie chart if a given categorycal exposure.
plotLOD
: Draws a barchart with the amount of underLOD values.
plotMissings
: Draws a barplot with the amount of missing values.
standardize
: Standardization of exposures.
Summary
: Summary of both continuous and categorical exposures
tableLOD
: Returns a vector with the number of underLOD values
per exposure.
tableMissings
: Returns a vector with the number of missing values
per exposure.
trans
: Transformation of exposures.
assayData
Contains the exposures matrix with column number equal to
nrow(phenoData)
(see eSet, AssayData).
featureData
Contains the description of the exposures including the family where they belong (see eSet, AnnotatedDataFrame).
phenoData
Contains the phenotypes or variables experimentersupplied (see eSet, AnnotatedDataFrame).
readExposome
to create an ExposomeSet
from files, loadExposome
to create an ExposomeSet
from data.frames
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