Methods for ExperimentList objects

Source: R/AllGenerics.R, R/ELAccessors.R, R/ELApply.R, and 1 more

The ExperimentList class provides a family of methods to manage and process data from multiple experiments.

nexp(x, ...)

experiments(x, ...)

experimentNames(x, ...)

experimentNames(x, ...) <- value

experimentData(x, ...)

experimentData(x, ...) <- value

elapply(x, ...)

# S4 method for ExperimentList
experimentData(x)

# S4 method for ExperimentList
experimentData(x) <- value

# S4 method for ExperimentList
nexp(x)

# S4 method for ExperimentList
experimentNames(x)

# S4 method for ExperimentList
experimentNames(x) <- value

# S4 method for SummarizedExperimentList,ANY,ANY,ANY
[(x, i, j, ..., exp, drop = TRUE)

# S4 method for RangedSummarizedExperimentList,ANY,ANY,ANY
[(x, i, j, ..., exp, drop = TRUE)

# S4 method for SingleCellExperimentList,ANY,ANY,ANY
[(x, i, j, ..., exp, drop = TRUE)

# S4 method for SpatialExperimentList,ANY,ANY,ANY
[(x, i, j, ..., exp, drop = TRUE)

# S4 method for ExperimentList
experiments(x, change.names = TRUE)

# S4 method for ExperimentList
elapply(x, FUN, ..., check.names = TRUE, change.names = TRUE)

# S4 method for SummarizedExperimentList
show(object)

# S4 method for RangedSummarizedExperimentList
show(object)

# S4 method for SingleCellExperimentList
show(object)

# S4 method for SpatialExperimentList
show(object)

Arguments

x

A SummarizedExperimentList, RangedSummarizedExperimentList, SingleCellExperimentList, or SpatialExperimentList object.

...

Further arguments to be passed to or from other methods.

value

Replacement value for replacement methods.

i

A subscript that can act to subset the rows of x.

j

A subscript that can act to subset the columns of x.

exp

A subscript that can act to subset experiments from x.

drop

A logical(1), ignored by these methods.

change.names

a logical indicating whether column names of columns in each individual experiment object should be concatenated with experiment names to ensure unique column names (default is TRUE).

FUN

The function to be applied to each element of x: see ‘Details’.

check.names

a logical specifying whether names of experiments should be checked against row names of experimentData (default is TRUE).

object

A SummarizedExperimentList, RangedSummarizedExperimentList, SingleCellExperimentList, or SpatialExperimentList object.

Value

Return value varies depending on method, as described below.

Details

Additional details for each type of data attribute are provided below.

Constructor

using the ExperimentList function documented in ?ExperimentList.

Accessors

x is a ExperimentList object.
experimentData(x), experimentData(x) <- value:

Get or set the experiment data. value is a DataFrame object. Row names of value must be NULL or consistent with the existing experiment names of x.

colWithExperimentData(x):

Get the column data merged with experiment data.

nexp(x):

Get the number of experiments in the ExperimentList object.

experimentNames(x), experimentNames(x) <- value:

Get or set the names of experiments.

experiments(x):

Get a list of the experiments (for example, a list of SummarizedExperiments).

Subsetting

x is a ExperimentList object.
x[i, j, exp]:

Create or replace a subset of x. i, j, exp can be numeric, logical, character, or missing.

subset(x, subset, select, experiment):

Create a subset of x using an expression subset referring to columns of rowData(x) and / or select referring to column names of colData(x) and / or experiment referring to column names of experimentData(x).

Apply

x is a ExperimentList object.
elapply(x, FUN, ..., simplify = TRUE, check.names = TRUE, change.names = TRUE):

Apply functions to each experiment within an ExperimentList and potentially simplify the results.

See also

ExperimentList, SummarizedExperiment, RangedSummarizedExperiment, SingleCellExperiment, SpatialExperiment

Examples

example(ExperimentList)
#> 
#> ExprmL> nrows <- 200; ncols <- 6
#> 
#> ExprmL> #Experiment 1
#> ExprmL> counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
#> 
#> ExprmL> colData <- DataFrame(Treatment=rep(c("ChIP", "Input"), 3),
#> ExprmL+                      row.names=LETTERS[1:6])
#> 
#> ExprmL> se1 <- SummarizedExperiment(assays=SimpleList(counts=counts),
#> ExprmL+                             colData=colData)
#> 
#> ExprmL> #Experiment 2
#> ExprmL> counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
#> 
#> ExprmL> colData <- DataFrame(Treatment=rep(c("ChIP", "Input"), 3),
#> ExprmL+                      row.names=LETTERS[1:6])
#> 
#> ExprmL> se2 <- SummarizedExperiment(assays=SimpleList(counts=counts),
#> ExprmL+                             colData=colData)
#> 
#> ExprmL> #Experiment annotation
#> ExprmL> experimentData <- DataFrame(age = c(36, 72),
#> ExprmL+                             sex = c("F", "M"),
#> ExprmL+                             row.names = c("PatientA", "PatientB"))
#> 
#> ExprmL> #Create ExperimentList
#> ExprmL> experiments = SimpleList("PatientA" = se1, "PatientB" = se2)
#> 
#> ExprmL> el = ExperimentList(experiments = experiments,
#> ExprmL+                     experimentData = experimentData)
#> 
#> ExprmL> el
#> ExperimentList with 2 SummarizedExperiments
#> class: SummarizedExperimentList 
#> dim: 200 12 
#> metadata(0):
#> assays(1): counts
#> rownames: NULL
#> rowData names(0):
#> colnames(12): PatientA.A PatientA.B ... PatientB.E PatientB.F
#> colData names(1): Treatment
#> experiments: 2
#> experimentNames (2): PatientA PatientB
#> experimentData names (2): age sex

nexp(el)
#> [1] 2
experimentData(el)
#> DataFrame with 2 rows and 2 columns
#>                age         sex
#>          <numeric> <character>
#> PatientA        36           F
#> PatientB        72           M
colData(el, experimentData = TRUE)
#> DataFrame with 12 rows and 3 columns
#>              Treatment       age         sex
#>            <character> <numeric> <character>
#> PatientA.A        ChIP        36           F
#> PatientA.B       Input        36           F
#> PatientA.C        ChIP        36           F
#> PatientA.D       Input        36           F
#> PatientA.E        ChIP        36           F
#> ...                ...       ...         ...
#> PatientB.B       Input        72           M
#> PatientB.C        ChIP        72           M
#> PatientB.D       Input        72           M
#> PatientB.E        ChIP        72           M
#> PatientB.F       Input        72           M
experimentNames(el)
#> [1] "PatientA" "PatientB"
el[1:5, 1:5]
#> ExperimentList with 2 SummarizedExperiments
#> class: SummarizedExperimentList 
#> dim: 5 5 
#> metadata(0):
#> assays(1): counts
#> rownames: NULL
#> rowData names(0):
#> colnames(5): PatientA.A PatientA.B PatientA.C PatientA.D PatientA.E
#> colData names(1): Treatment
#> experiments: 2
#> experimentNames (2): PatientA PatientB
#> experimentData names (2): age sex
el[, exp = 'PatientA']
#> ExperimentList with 1 SummarizedExperiments
#> class: SummarizedExperimentList 
#> dim: 200 6 
#> metadata(0):
#> assays(1): counts
#> rownames: NULL
#> rowData names(0):
#> colnames(6): PatientA.A PatientA.B ... PatientA.E PatientA.F
#> colData names(1): Treatment
#> experiments: 1
#> experimentNames (1): PatientA
#> experimentData names (2): age sex
elapply(el, dim)
#> $PatientA
#> [1] 200   6
#> 
#> $PatientB
#> [1] 200   6
#>