Package 'MultimodalExperiment'

Title: Integrative Bulk and Single-Cell Experiment Container
Description: MultimodalExperiment is an S4 class that integrates bulk and single-cell experiment data; it is optimally storage-efficient, and its methods are exceptionally fast. It effortlessly represents multimodal data of any nature and features normalized experiment, subject, sample, and cell annotations, which are related to underlying biological experiments through maps. Its coordination methods are opt-in and employ database-like join operations internally to deliver fast and flexible management of multimodal data.
Authors: Lucas Schiffer [aut, cre]
Maintainer: Lucas Schiffer <[email protected]>
License: Artistic-2.0
Version: 1.5.0
Built: 2024-07-12 04:48:40 UTC
Source: https://github.com/bioc/MultimodalExperiment

Help Index

MultimodalExperiment Annotation Methods

Description

joinAnnotations joins all annotations into an unnormalized DataFrame object.

Usage

## S4 method for signature 'MultimodalExperiment'
joinAnnotations(x)

Arguments

x

a MultimodalExperiment object

Value

joinAnnotations returns a DataFrame object.

See Also

browseVignettes("MultimodalExperiment")

Examples

ME <-
    MultimodalExperiment()

bulkExperiments(ME) <-
    ExperimentList(
        pbRNAseq = pbRNAseq
    )

singleCellExperiments(ME) <-
    ExperimentList(
        scADTseq = scADTseq,
        scRNAseq = scRNAseq
    )

subjectMap(ME)[["subject"]] <-
    "SUBJECT-1"

sampleMap(ME)[["subject"]] <-
    "SUBJECT-1"

cellMap(ME)[["sample"]] <-
    "SAMPLE-1"

ME <-
    propagate(ME)

experimentData(ME)[["published"]] <-
    c(NA_character_, "2018-11-19", "2018-11-19") |>
    as.Date()

subjectData(ME)[["condition"]] <-
    as.character("healthy")

sampleData(ME)[["sampleType"]] <-
    as.character("peripheral blood mononuclear cells")

cellType <- function(x) {
    if (x[["CD4"]] > 0L) {
        return("T Cell")
    }

    if (x[["CD14"]] > 0L) {
        return("Monocyte")
    }

    if (x[["CD19"]] > 0L) {
        return("B Cell")
    }

    if (x[["CD56"]] > 0L) {
        return("NK Cell")
    }

    NA_character_
}

cellData(ME)[["cellType"]] <-
    experiment(ME, "scADTseq") |>
    apply(2L, cellType)

joinAnnotations(ME)

MultimodalExperiment Coordination Methods

Description

Propagate or harmonize indices of a MultimodalExperiment object.

Usage

## S4 method for signature 'MultimodalExperiment'
propagate(x)

## S4 method for signature 'MultimodalExperiment'
harmonize(x)

Arguments

x

a MultimodalExperiment object

Details

propagate inserts experiment, subject, sample, and cell indices into all relevant tables by taking their union and adding missing indices.

harmonize deletes experiment, subject, sample, and cell indices from all relevant tables by taking their intersection and removing extraneous indices.

Value

propagate returns a MultimodalExperiment object.

harmonize returns a MultimodalExperiment object.

See Also

browseVignettes("MultimodalExperiment")

Examples

ME <-
    MultimodalExperiment()

bulkExperiments(ME) <-
    ExperimentList(
        pbRNAseq = pbRNAseq
    )

singleCellExperiments(ME) <-
    ExperimentList(
        scADTseq = scADTseq,
        scRNAseq = scRNAseq
    )

subjectMap(ME)[["subject"]] <-
    "SUBJECT-1"

sampleMap(ME)[["subject"]] <-
    "SUBJECT-1"

cellMap(ME)[["sample"]] <-
    "SAMPLE-1"

ME <-
    propagate(ME)

experimentData(ME)[["published"]] <-
    c(NA_character_, "2018-11-19", "2018-11-19") |>
    as.Date()

subjectData(ME)[["condition"]] <-
    as.character("healthy")

sampleData(ME)[["sampleType"]] <-
    as.character("peripheral blood mononuclear cells")

cellType <- function(x) {
    if (x[["CD4"]] > 0L) {
        return("T Cell")
    }

    if (x[["CD14"]] > 0L) {
        return("Monocyte")
    }

    if (x[["CD19"]] > 0L) {
        return("B Cell")
    }

    if (x[["CD56"]] > 0L) {
        return("NK Cell")
    }

    NA_character_
}

cellData(ME)[["cellType"]] <-
    experiment(ME, "scADTseq") |>
    apply(2L, cellType)

isMonocyte <-
    cellData(ME)[["cellType"]] %in% "Monocyte"

cellData(ME) <-
    cellData(ME)[isMonocyte, , drop = FALSE]

harmonize(ME)

MultimodalExperiment Example Data

Description

Human peripheral blood mononuclear cells (PBMCs) from a single healthy donor were profiled by cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) to generate single-cell antibody-derived tag sequencing (scADTseq) and single-cell RNA sequencing (scRNAseq) data simultaneously; the scRNAseq data was summed into pseudo-bulk RNA sequencing (pbRNAseq) data. The dimensions of resulting matrices were reduced to conserve storage because these data are only used to demonstrate the functionality of the MultimodalExperiment class.

Usage

pbRNAseq

scADTseq

scRNAseq

Format

An object of class matrix (inherits from array) with 3000 rows and 1 columns.

An object of class matrix (inherits from array) with 8 rows and 5000 columns.

An object of class matrix (inherits from array) with 3000 rows and 5000 columns.

Source

PBMCs of a Healthy Donor - 5' Gene Expression with a Panel of TotalSeq™-C Antibodies, Single Cell Immune Profiling Dataset by Cell Ranger 3.0.0, 10x Genomics, (2018, November 19).

Examples

pbRNAseq[1:4, 1:1, drop = FALSE]

scADTseq[1:4, 1:4, drop = FALSE]

scRNAseq[1:4, 1:4, drop = FALSE]

MultimodalExperiment Experiment Methods

Description

Extract or replace experiments of a MultimodalExperiment object by index, name, or type.

Usage

## S4 method for signature 'MultimodalExperiment'
experiment(x, i)

## S4 replacement method for signature 'MultimodalExperiment'
experiment(x, i) <- value

## S4 method for signature 'MultimodalExperiment'
bulkExperiments(x)

## S4 replacement method for signature 'MultimodalExperiment'
bulkExperiments(x) <- value

## S4 method for signature 'MultimodalExperiment'
singleCellExperiments(x)

## S4 replacement method for signature 'MultimodalExperiment'
singleCellExperiments(x) <- value

Arguments

x

a MultimodalExperiment object
i

an integer or character index
value

a replacement value

Details

The term matrix-like objects refers to matrix objects or Bioconductor S4 objects that contain them ( SummarizedExperiment, SingleCellExperiment, etc.) where rows represent features and columns represent observations.

Value

experiment returns a matrix-like object.

bulkExperiments returns an ExperimentList of matrix-like objects.

singleCellExperiments returns an ExperimentList of matrix-like objects.

See Also

browseVignettes("MultimodalExperiment")

Examples

ME <-
    MultimodalExperiment()

bulkExperiments(ME) <-
    ExperimentList(
        pbRNAseq = pbRNAseq
    )

singleCellExperiments(ME) <-
    ExperimentList(
        scADTseq = scADTseq,
        scRNAseq = scRNAseq
    )

subjectMap(ME)[["subject"]] <-
    "SUBJECT-1"

sampleMap(ME)[["subject"]] <-
    "SUBJECT-1"

cellMap(ME)[["sample"]] <-
    "SAMPLE-1"

ME <-
    propagate(ME)

experimentData(ME)[["published"]] <-
    c(NA_character_, "2018-11-19", "2018-11-19") |>
    as.Date()

subjectData(ME)[["condition"]] <-
    as.character("healthy")

sampleData(ME)[["sampleType"]] <-
    as.character("peripheral blood mononuclear cells")

cellType <- function(x) {
    if (x[["CD4"]] > 0L) {
        return("T Cell")
    }

    if (x[["CD14"]] > 0L) {
        return("Monocyte")
    }

    if (x[["CD19"]] > 0L) {
        return("B Cell")
    }

    if (x[["CD56"]] > 0L) {
        return("NK Cell")
    }

    NA_character_
}

cellData(ME)[["cellType"]] <-
    experiment(ME, "scADTseq") |>
    apply(2L, cellType)

experiment(ME, 2L) <-
    experiment(ME, 2L)[1:4, 1:4]

experiment(ME, 2L)

experiment(ME, "scRNAseq") <-
    experiment(ME, "scRNAseq")[1:4, 1:4]

experiment(ME, "scRNAseq")

bulkExperiments(ME) <-
    bulkExperiments(ME)[1L]

bulkExperiments(ME)

singleCellExperiments(ME) <-
    singleCellExperiments(ME)[2L]

singleCellExperiments(ME)

MultimodalExperiment Map Methods

Description

joinMaps joins all maps into an unnormalized DataFrame object.

Usage

## S4 method for signature 'MultimodalExperiment'
joinMaps(x)

Arguments

x

a MultimodalExperiment object

Value

joinMaps returns a DataFrame object.

See Also

browseVignettes("MultimodalExperiment")

Examples

ME <-
    MultimodalExperiment()

bulkExperiments(ME) <-
    ExperimentList(
        pbRNAseq = pbRNAseq
    )

singleCellExperiments(ME) <-
    ExperimentList(
        scADTseq = scADTseq,
        scRNAseq = scRNAseq
    )

subjectMap(ME)[["subject"]] <-
    "SUBJECT-1"

sampleMap(ME)[["subject"]] <-
    "SUBJECT-1"

cellMap(ME)[["sample"]] <-
    "SAMPLE-1"

ME <-
    propagate(ME)

experimentData(ME)[["published"]] <-
    c(NA_character_, "2018-11-19", "2018-11-19") |>
    as.Date()

subjectData(ME)[["condition"]] <-
    as.character("healthy")

sampleData(ME)[["sampleType"]] <-
    as.character("peripheral blood mononuclear cells")

cellType <- function(x) {
    if (x[["CD4"]] > 0L) {
        return("T Cell")
    }

    if (x[["CD14"]] > 0L) {
        return("Monocyte")
    }

    if (x[["CD19"]] > 0L) {
        return("B Cell")
    }

    if (x[["CD56"]] > 0L) {
        return("NK Cell")
    }

    NA_character_
}

cellData(ME)[["cellType"]] <-
    experiment(ME, "scADTseq") |>
    apply(2L, cellType)

joinMaps(ME)

MultimodalExperiment Constructor Function

Description

MultimodalExperiment constructs a MultimodalExperiment object.

Usage

MultimodalExperiment(
    experimentData = DataFrame(),
    subjectData = DataFrame(),
    sampleData = DataFrame(),
    cellData = DataFrame(),
    experimentMap = DataFrame(
        type = character(),
        experiment = character()
    ),
    subjectMap = DataFrame(
        experiment = character(),
        subject = character()
    ),
    sampleMap = DataFrame(
        subject = character(),
        sample = character()
    ),
    cellMap = DataFrame(
        sample = character(),
        cell = character()
    ),
    experiments = ExperimentList(),
    metadata = list()
)

Arguments

experimentData

a DataFrame of experiment annotations with experiment indices as rownames
subjectData

a DataFrame of subject annotations with subject indices as rownames
sampleData

a DataFrame of sample annotations with sample indices as rownames
cellData

a DataFrame of cell annotations with cell indices as rownames
experimentMap

a DataFrame of type (bulk or single-cell) to experiment (index) mappings
subjectMap

a DataFrame of experiment (index) to subject (index) mappings
sampleMap

a DataFrame of subject (index) to sample (index) mappings
cellMap

a DataFrame of sample (index) to cell (index) mappings
experiments

an ExperimentList of matrix-like objects
metadata

a list of metadata objects

Details

The term matrix-like objects refers to matrix objects or Bioconductor S4 objects that contain them ( SummarizedExperiment, SingleCellExperiment, etc.) where rows represent features and columns represent observations.

Value

MultimodalExperiment returns a MultimodalExperiment object.

See Also

browseVignettes("MultimodalExperiment")

Examples

MultimodalExperiment()

MultimodalExperiment Class Definition

Description

MultimodalExperiment is an S4 class that integrates bulk and single-cell experiment data; it is optimally storage-efficient, and its methods are exceptionally fast. It effortlessly represents multimodal data of any nature and features normalized experiment, subject, sample, and cell annotations, which are related to underlying biological experiments through maps. Its coordination methods are opt-in and employ database-like join operations internally to deliver fast and flexible management of multimodal data.

Details

The term matrix-like objects refers to matrix objects or Bioconductor S4 objects that contain them ( SummarizedExperiment, SingleCellExperiment, etc.) where rows represent features and columns represent observations.

Slots

experimentData

a DataFrame of experiment annotations with experiment indices as rownames

subjectData

a DataFrame of subject annotations with subject indices as rownames

sampleData

a DataFrame of sample annotations with sample indices as rownames

cellData

a DataFrame of cell annotations with cell indices as rownames

experimentMap

a DataFrame of type (bulk or single-cell) to experiment (index) mappings

subjectMap

a DataFrame of experiment (index) to subject (index) mappings

sampleMap

a DataFrame of subject (index) to sample (index) mappings

cellMap

a DataFrame of sample (index) to cell (index) mappings

experiments

an ExperimentList of matrix-like objects

metadata

a list of metadata objects

See Also

browseVignettes("MultimodalExperiment")

MultimodalExperiment Name Methods

Description

Extract or replace names of a MultimodalExperiment object.

Usage

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

## S4 replacement method for signature 'MultimodalExperiment'
names(x) <- value

## S4 method for signature 'MultimodalExperiment'
rownames(x)

## S4 replacement method for signature 'MultimodalExperiment'
rownames(x) <- value

## S4 method for signature 'MultimodalExperiment'
colnames(x)

## S4 replacement method for signature 'MultimodalExperiment,ANY'
colnames(x) <- value

## S4 method for signature 'MultimodalExperiment'
dimnames(x)

## S4 replacement method for signature 'MultimodalExperiment,ANY'
dimnames(x) <- value

## S4 method for signature 'MultimodalExperiment'
experimentNames(x)

## S4 replacement method for signature 'MultimodalExperiment'
experimentNames(x) <- value

Arguments

x

a MultimodalExperiment object
value

a replacement value

Value

names returns a CharacterList object.

rownames returns a CharacterList object.

colnames returns a CharacterList object.

dimnames returns a list object.

experimentNames returns a character vector.

See Also

browseVignettes("MultimodalExperiment")

Examples

ME <-
    MultimodalExperiment()

bulkExperiments(ME) <-
    ExperimentList(
        pbRNAseq = pbRNAseq
    )

singleCellExperiments(ME) <-
    ExperimentList(
        scADTseq = scADTseq,
        scRNAseq = scRNAseq
    )

subjectMap(ME)[["subject"]] <-
    "SUBJECT-1"

sampleMap(ME)[["subject"]] <-
    "SUBJECT-1"

cellMap(ME)[["sample"]] <-
    "SAMPLE-1"

ME <-
    propagate(ME)

experimentData(ME)[["published"]] <-
    c(NA_character_, "2018-11-19", "2018-11-19") |>
    as.Date()

subjectData(ME)[["condition"]] <-
    as.character("healthy")

sampleData(ME)[["sampleType"]] <-
    as.character("peripheral blood mononuclear cells")

cellType <- function(x) {
    if (x[["CD4"]] > 0L) {
        return("T Cell")
    }

    if (x[["CD14"]] > 0L) {
        return("Monocyte")
    }

    if (x[["CD19"]] > 0L) {
        return("B Cell")
    }

    if (x[["CD56"]] > 0L) {
        return("NK Cell")
    }

    NA_character_
}

cellData(ME)[["cellType"]] <-
    experiment(ME, "scADTseq") |>
    apply(2L, cellType)

names(ME) <-
    names(ME) |>
    tolower()

names(ME)

rownames(ME) <-
    rownames(ME) |>
    toupper()

rownames(ME)

colnames(ME) <-
    colnames(ME) |>
    tolower()

colnames(ME)

dimnames(ME)[[2L]] <-
    dimnames(ME)[[2L]] |>
    toupper()

dimnames(ME)[[2L]]

experimentNames(ME) <-
    experimentNames(ME) |>
    gsub(pattern = "seq", replacement = "-seq")

experimentNames(ME)

MultimodalExperiment Slot Methods

Description

Extract or replace slots of a MultimodalExperiment object.

Usage

## S4 method for signature 'MultimodalExperiment'
experimentData(object)

## S4 replacement method for signature 'MultimodalExperiment'
experimentData(object) <- value

## S4 method for signature 'MultimodalExperiment'
subjectData(object)

## S4 replacement method for signature 'MultimodalExperiment'
subjectData(object) <- value

## S4 method for signature 'MultimodalExperiment'
sampleData(object)

## S4 replacement method for signature 'MultimodalExperiment'
sampleData(object) <- value

## S4 method for signature 'MultimodalExperiment'
cellData(object)

## S4 replacement method for signature 'MultimodalExperiment'
cellData(object) <- value

## S4 method for signature 'MultimodalExperiment'
experimentMap(object)

## S4 replacement method for signature 'MultimodalExperiment'
experimentMap(object) <- value

## S4 method for signature 'MultimodalExperiment'
subjectMap(object)

## S4 replacement method for signature 'MultimodalExperiment'
subjectMap(object) <- value

## S4 method for signature 'MultimodalExperiment'
sampleMap(object)

## S4 replacement method for signature 'MultimodalExperiment'
sampleMap(object) <- value

## S4 method for signature 'MultimodalExperiment'
cellMap(object)

## S4 replacement method for signature 'MultimodalExperiment'
cellMap(object) <- value

## S4 method for signature 'MultimodalExperiment'
experiments(object)

## S4 replacement method for signature 'MultimodalExperiment'
experiments(object) <- value

Arguments

object

a MultimodalExperiment object
value

a replacement value

Value

Extract methods return the value of the slot.

See Also

browseVignettes("MultimodalExperiment")

Examples

ME <-
    MultimodalExperiment()

bulkExperiments(ME) <-
    ExperimentList(
        pbRNAseq = pbRNAseq
    )

singleCellExperiments(ME) <-
    ExperimentList(
        scADTseq = scADTseq,
        scRNAseq = scRNAseq
    )

subjectMap(ME)[["subject"]] <-
    "SUBJECT-1"

sampleMap(ME)[["subject"]] <-
    "SUBJECT-1"

cellMap(ME)[["sample"]] <-
    "SAMPLE-1"

ME <-
    propagate(ME)

experimentData(ME)[["published"]] <-
    c(NA_character_, "2018-11-19", "2018-11-19") |>
    as.Date()

subjectData(ME)[["condition"]] <-
    as.character("healthy")

sampleData(ME)[["sampleType"]] <-
    as.character("peripheral blood mononuclear cells")

cellType <- function(x) {
    if (x[["CD4"]] > 0L) {
        return("T Cell")
    }

    if (x[["CD14"]] > 0L) {
        return("Monocyte")
    }

    if (x[["CD19"]] > 0L) {
        return("B Cell")
    }

    if (x[["CD56"]] > 0L) {
        return("NK Cell")
    }

    NA_character_
}

cellData(ME)[["cellType"]] <-
    experiment(ME, "scADTseq") |>
    apply(2L, cellType)

experimentData(ME)

subjectData(ME)

sampleData(ME)

cellData(ME)

experimentMap(ME)

subjectMap(ME)

sampleMap(ME)

cellMap(ME)

experiments(ME)

MultimodalExperiment Subset Methods

Description

Extract or replace parts of a MultimodalExperiment object.

Usage

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

## S4 replacement method for signature 'MultimodalExperiment,ANY,ANY,ANY'
x[i, j] <- value

Arguments

x

a MultimodalExperiment object
i

a list, List, LogicalList, IntegerList, or CharacterList of elements to extract or replace
j

a list, List, LogicalList, IntegerList, or CharacterList of elements to extract or replace
...

ignored, required by generic
drop

ignored, required by generic
value

a replacement value

Value

[ returns a MultimodalExperiment object.

See Also

browseVignettes("MultimodalExperiment")

Examples

ME <-
    MultimodalExperiment()

bulkExperiments(ME) <-
    ExperimentList(
        pbRNAseq = pbRNAseq
    )

singleCellExperiments(ME) <-
    ExperimentList(
        scADTseq = scADTseq,
        scRNAseq = scRNAseq
    )

subjectMap(ME)[["subject"]] <-
    "SUBJECT-1"

sampleMap(ME)[["subject"]] <-
    "SUBJECT-1"

cellMap(ME)[["sample"]] <-
    "SAMPLE-1"

ME <-
    propagate(ME)

experimentData(ME)[["published"]] <-
    c(NA_character_, "2018-11-19", "2018-11-19") |>
    as.Date()

subjectData(ME)[["condition"]] <-
    as.character("healthy")

sampleData(ME)[["sampleType"]] <-
    as.character("peripheral blood mononuclear cells")

cellType <- function(x) {
    if (x[["CD4"]] > 0L) {
        return("T Cell")
    }

    if (x[["CD14"]] > 0L) {
        return("Monocyte")
    }

    if (x[["CD19"]] > 0L) {
        return("B Cell")
    }

    if (x[["CD56"]] > 0L) {
        return("NK Cell")
    }

    NA_character_
}

cellData(ME)[["cellType"]] <-
    experiment(ME, "scADTseq") |>
    apply(2L, cellType)

i <-
    rownames(ME) |>
    endoapply(sample, 4L)

j <-
    colnames(ME) |>
    endoapply(sample, 1L)

ME[i, j] <-
    0L

experiment(ME[i, j], "pbRNAseq")

experiment(ME[i, j], "scADTseq")

experiment(ME[i, j], "scRNAseq")