MultiDataSet-class {MultiDataSet} | R Documentation |
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 |
|
set |
Object derived from |
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 |
|
gexpSet |
|
... |
Further arguments passed to add_rse or add_se |
rnaSet |
|
methySet |
|
snpSet |
|
x |
|
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 |
|
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
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.
createMultiDataSet()