MultiDataSet (version 1.0.2)

MultiDataSet-class: MultiDataSet instances

Description

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

Usage

"add_eset"(object, set, dataset.type, dataset.name = NULL, warnings = TRUE, overwrite = FALSE, GRanges)
"add_genexp"(object, gexpSet, ...)
"add_rnaseq"(object, rnaSet, ...)
"add_methy"(object, methySet, ...)
"add_methy"(object, methySet, ...)
"add_rse"(object, set, dataset.type, dataset.name = NULL, warnings = TRUE, overwrite = FALSE)
"add_snps"(object, snpSet, ...)
"as.list"(x)
"assayData"(object)
"commonIds"(object)
"commonSamples"(object)
createMultiDataSet()
"fData"(object)
"length"(x)
"names"(x)
"sampleNames"(object)
"pData"(object)
"rowRanges"(x)
"[["(x, i)
"["(x, i, j, k, ..., drop = FALSE)

Arguments

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

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_eset.

rnaSet

ExpressionSet to be used to fill the slot.

methySet

MethylationSet to be used to fill the slot.

snpSet

SnpSet to be used to fill the slot.

x

MultiDataSet

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

...

Value

MultiDataSet

Methods (by generic)

• 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.
• add_methy: Method to add a slot of methylation to MultiDataSet.
• add_rse: Method to add a RangedSummarizedExperiment to MultiDataSet.
• add_snps: Method to add a slot of SNPs to MultiDataSet.
• as.list: Returns a list with the first matrix of each dataset.
• assayData: Retrieve all assay data blocks.
• commonIds: Get the name of the ids common to all datasets
• commonSamples: Get a MultiDataSet only with the samples present in all the tables
• fData: Retrieve information on features.
• length: Returns the number of sets into the object.
• names: Get the names of the slots.
• sampleNames: Get sample names
• pData: Retrieve information on experimental phenotypes.
• rowRanges: Retrieve information on feature ranges.
• [[: Get a set from a slot
• [: Subset a MultiDataSet

Slots

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.

return_method

List of functions used to create the original object.

Details

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

See Also

add_eset, add_rse

Examples

createMultiDataSet()