MultiDataSet-class: MultiDataSet instances
In isglobal-brge/MultiDataSet: Implementation of MultiDataSet and ResultSet

Description Usage Arguments Details Value Methods (by generic) Slots See Also Examples

The class MultiDataSet is a superior class to store multiple datasets in form of triplets (assayData-phenoData-featureData). The datasets can be eSet or SummarizedExperiment derived or matrices.

## S4 method for signature 'MultiDataSet,eSet'
add_eset(
  object,
  set,
  dataset.type,
  dataset.name = NULL,
  sample.tables = "protocolData",
  feature.tables = NULL,
  warnings = TRUE,
  overwrite = FALSE,
  GRanges
)

## S4 method for signature 'MultiDataSet,ExpressionSet'
add_genexp(object, gexpSet, ...)

## S4 method for signature 'MultiDataSet,ExpressionSet'
add_rnaseq(object, rnaSet, ...)

## S4 method for signature 'MultiDataSet,GenomicRatioSet'
add_methy(object, methySet, ...)

## S4 method for signature 'MultiDataSet,RangedSummarizedExperiment'
add_rse(
  object,
  set,
  dataset.type,
  dataset.name = NULL,
  sample.tables = NULL,
  feature.tables = "elementMetadata",
  warnings = TRUE,
  overwrite = FALSE
)

## S4 method for signature 'MultiDataSet,SummarizedExperiment'
add_se(
  object,
  set,
  dataset.type,
  dataset.name = NULL,
  sample.tables = NULL,
  feature.tables = "elementMetadata",
  warnings = TRUE,
  overwrite = FALSE,
  GRanges
)

## S4 method for signature 'MultiDataSet,SnpSet'
add_snps(object, snpSet, ...)

## S4 method for signature 'MultiDataSet,matrix'
add_table(
  object,
  set,
  dataset.type,
  dataset.name = NULL,
  warnings = TRUE,
  overwrite = FALSE
)

## S4 method for signature 'MultiDataSet'
as.list(x)

## S4 method for signature 'MultiDataSet'
commonIds(object)

## S4 method for signature 'MultiDataSet'
commonSamples(object, unify.names = FALSE)

createMultiDataSet()

## S4 method for signature 'MultiDataSet'
dims(x)

## S4 method for signature 'MultiDataSet'
w_iclusterplus(object, commonSamples = TRUE, ...)

## S4 method for signature 'MultiDataSet'
length(x)

## S4 method for signature 'MultiDataSet'
w_mcia(object, ...)

## S4 method for signature 'MultiDataSet'
names(x)

## S4 method for signature 'MultiDataSet'
ncol(x)

## S4 method for signature 'MultiDataSet'
nrow(x)

## S4 method for signature 'MultiDataSet'
rowRangesElements(object)

## S4 method for signature 'MultiDataSet'
sampleNames(object)

## S4 method for signature 'MultiDataSet'
assayData(object)

## S4 method for signature 'MultiDataSet'
fData(object)

## S4 method for signature 'MultiDataSet'
featureData(object)

## S4 method for signature 'MultiDataSet'
pData(object)

## S4 method for signature 'MultiDataSet'
phenoData(object)

## S4 method for signature 'MultiDataSet'
rowRanges(x)

## S4 method for signature 'MultiDataSet,ANY,ANY'
x[[i]]

## S4 method for signature 'MultiDataSet,ANY,ANY,ANY'
x[i, j, k, ..., drop = FALSE]

## S4 method for signature 'MultiDataSet'
subset(x, feat, phe, warnings = TRUE, keep = TRUE)

`object`	`MultiDataSet`
`set`	Object derived from `eSet` to be used to fill the slot.
`dataset.type`	Character with the type of data of the omic set (e.g. expression, methylation...)
`dataset.name`	Character with the specific name for this set (NULL by default). It is useful when there
`sample.tables`	Character with the names of the slots with sample data besides phenoData.
`feature.tables`	Character with the names of the slots with feature data besides featureData.
`warnings`	Logical to indicate if warnings will be displayed.
`overwrite`	Logical to indicate if the set stored in the slot will be overwritten.
`GRanges`	`GenomicRanges` to be included in rowRanges slot.
`gexpSet`	`ExpressionSet` to be used to fill the slot.
`...`	Further arguments passed to add_rse or add_se
`rnaSet`	`ExpressionSet` to be used to fill the slot.
`methySet`	`GenomicRatioSet` to be used to fill the slot.
`snpSet`	`SnpSet` to be used to fill the slot.
`x`	`MultiDataSet`
`unify.names`	Logical indicating if sample names of the sets should be unified.
`commonSamples`	Logical to indicate if common samples are selected
`i`	Character corresponding to selected sample names. They should match the id column of phenoData.
`j`	Character with the name of the selected tables.
`k`	`GenomicRange` used to filter the features.
`drop`	If TRUE, sets with no samples or features will be discarded
`feat`	Logical expression indicating features to keep
`phe`	Logical expression indicating the phenotype of the samples to keep
`keep`	If FALSE, sets where the expression cannot be evaluated will be discarded.

The names of the three lists (assayData, phenoData and featureData) must be the same.

MultiDataSet

add_eset: Method to add an eSet to MultiDataSet.
add_genexp: Method to add a slot of expression to MultiDataSet.
add_rnaseq: Method to add a slot of (RNASeq) expression to MultiDataSet.
add_methy: Method to add a slot of methylation to MultiDataSet from a GenomicRatioSet.
add_rse: Method to add a RangedSummarizedExperiment to MultiDataSet.
add_se: Method to add a SummarizedExperiment to MultiDataSet.
add_snps: Method to add a slot of SNPs to MultiDataSet.
add_table: Method to add a matrix to MultiDataSet.
as.list: Returns a list with the first matrix of each dataset.
commonIds: Get the name of the ids common to all datasets
commonSamples: Get a MultiDataSet only with the samples present in all the tables
dims: Returns the dimensions of the sets
w_iclusterplus: Apply iClusterPlus clustering method to a MultiDataSet object
length: Returns the number of sets into the object.
w_mcia: Apply mcia integration method to a MultiDataSet object
names: Get the names of the slots.
ncol: Get number of samples of each set
nrow: Get number of features of each set
rowRangesElements: Get the name of the datasets that have rowRanges
sampleNames: Get sample names
assayData: Retrieve all assay data blocks.
fData: Retrieve information on features.
featureData: Retrieve information on features.
pData: Retrieve information on experimental phenotypes
phenoData: Retrieve information on experimental phenotypes
rowRanges: Retrieve information on feature ranges.
[[: Get a set from a slot
[: Subset a MultiDataSet
subset: Filter a subset using feature ids or phenotypes

assayData: List of assayData elements.
phenoData: List of AnnotatedDataFrame containing the phenoData of each assayData.
featureData: List of AnnotatedDataFrame containing the featureData of each assayData.
rowRanges: List of GenomicRanges containing the rowRanges of each assayData.
extraData: List of other slots of the original object.
return_method: List of functions used to create the original object.