MultiDataSet-class: MultiDataSet instances

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

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

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## S4 method for signature 'MultiDataSet,eSet'
add_eset(object, set, dataset.type,
  dataset.name = 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,MethylationSet'
add_methy(object, methySet, ...)

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

## 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, warnings = TRUE, overwrite = FALSE)

## S4 method for signature 'MultiDataSet,SummarizedExperiment'
add_se(object, set, dataset.type,
  dataset.name = NULL, 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(object)

## 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)

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

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.

Details

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

Value

MultiDataSet

MultiDataSet

Methods (by generic)

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.

See Also

add_eset, add_rse

Examples

1

Bioconductor-mirror/MultiDataSet documentation built on June 26, 2017, 10:25 p.m.