rowData and colData of subsets in ExperimentSubset objects

Get or set the rowData or colData of a subset by naming it with subsetName. Without subsetName, these methods act on the main object, as for the class x extends.

A subset stores only its own columns. With parentRowData = TRUE or parentColData = TRUE, the main object's columns come first, for the subset's rows or columns, and a subset's own column hides the main object's column of the same name, with a message if their values differ. When setting a subset's data, columns that came from the main object, in data read with parentRowData = TRUE or parentColData = TRUE, are left out with a message, so only the subset's own are stored. To add one column, use colData(x, subsetName = "name")$column <- values.

Usage

# S4 method for class 'SubsetRangedSummarizedExperiment'
rowData(x, use.names = TRUE, ...)

# S4 method for class 'SubsetRangedSummarizedExperiment'
colData(x, ...)

# S4 method for class 'SubsetRangedSummarizedExperiment'
rowData(x, ...) <- value

# S4 method for class 'SubsetRangedSummarizedExperiment,DataFrame'
colData(x, ...) <- value

# S4 method for class 'SubsetRangedSummarizedExperiment,NULL'
colData(x, ...) <- value

# S4 method for class 'SubsetRangedSummarizedExperiment,data.frame'
colData(x, ...) <- value

# S4 method for class 'SubsetRangedSummarizedExperiment,ANY'
colData(x, ...) <- value

# S4 method for class 'SubsetSingleCellExperiment'
rowData(x, use.names = TRUE, ...)

# S4 method for class 'SubsetSingleCellExperiment'
colData(x, ...)

# S4 method for class 'SubsetSingleCellExperiment'
rowData(x, ...) <- value

# S4 method for class 'SubsetSingleCellExperiment,DataFrame'
colData(x, ...) <- value

# S4 method for class 'SubsetSingleCellExperiment,NULL'
colData(x, ...) <- value

# S4 method for class 'SubsetSingleCellExperiment,data.frame'
colData(x, ...) <- value

# S4 method for class 'SubsetSingleCellExperiment,ANY'
colData(x, ...) <- value

# S4 method for class 'SubsetSummarizedExperiment'
rowData(x, use.names = TRUE, ...)

# S4 method for class 'SubsetSummarizedExperiment'
colData(x, ...)

# S4 method for class 'SubsetSummarizedExperiment'
rowData(x, ...) <- value

# S4 method for class 'SubsetSummarizedExperiment,DataFrame'
colData(x, ...) <- value

# S4 method for class 'SubsetSummarizedExperiment,NULL'
colData(x, ...) <- value

# S4 method for class 'SubsetSummarizedExperiment,data.frame'
colData(x, ...) <- value

# S4 method for class 'SubsetSummarizedExperiment,ANY'
colData(x, ...) <- value

# S4 method for class 'SubsetSpatialExperiment'
rowData(x, use.names = TRUE, ...)

# S4 method for class 'SubsetSpatialExperiment'
colData(x, ...)

# S4 method for class 'SubsetSpatialExperiment'
rowData(x, ...) <- value

# S4 method for class 'SubsetSpatialExperiment,DataFrame'
colData(x, ...) <- value

# S4 method for class 'SubsetSpatialExperiment,NULL'
colData(x, ...) <- value

# S4 method for class 'SubsetSpatialExperiment,data.frame'
colData(x, ...) <- value

# S4 method for class 'SubsetSpatialExperiment,ANY'
colData(x, ...) <- value

# S4 method for class 'SubsetTreeSummarizedExperiment'
rowData(x, use.names = TRUE, ...)

# S4 method for class 'SubsetTreeSummarizedExperiment'
colData(x, ...)

# S4 method for class 'SubsetTreeSummarizedExperiment'
rowData(x, ...) <- value

# S4 method for class 'SubsetTreeSummarizedExperiment,DataFrame'
colData(x, ...) <- value

# S4 method for class 'SubsetTreeSummarizedExperiment,NULL'
colData(x, ...) <- value

# S4 method for class 'SubsetTreeSummarizedExperiment,data.frame'
colData(x, ...) <- value

# S4 method for class 'SubsetTreeSummarizedExperiment,ANY'
colData(x, ...) <- value

Arguments

x

An ExperimentSubset object.

use.names

logical(1) Whether the rowData returned has row names. Default TRUE.

...

subsetName: character(1) Name of the subset whose data to get or set. Leave it out for the main object's.
parentRowData: logical(1) For rowData() of a subset, whether to include the main object's columns. Default FALSE.
parentColData: logical(1) For colData() of a subset, whether to include the main object's columns. Default FALSE.

Without subsetName, other arguments are passed on to the method of the class x extends.

value

A DataFrame with one row per row (rowData<-) or column (colData<-) of the subset or the main object, or NULL to remove all columns (a SpatialExperiment keeps its sample_id column). For a subset, a data.frame is also accepted and converted to a DataFrame; for the main object, colData<- with a data.frame is an error. For a subset, the rownames of value must be NULL or the subset's row names (rowData<-) or column names (colData<-), in the same order.

Value

rowData() and colData() return a DataFrame. The setters return x with the data set.

Examples

# an object with 10 genes and 20 cells
set.seed(1)
counts <- matrix(rpois(200, lambda = 5), nrow = 10)
rownames(counts) <- paste0("gene", 1:10)
colnames(counts) <- paste0("cell", 1:20)
es <- ExperimentSubset(list(counts = counts))
# a sample label for every cell of the main object
es$sample <- rep(c("A", "B"), each = 10)
# a subset of the first 5 genes and the first 8 cells
es <- createSubset(es, subsetName = "first", rows = 1:5, cols = 1:8)
# a cluster label for each of the subset's 8 cells
colData(es, subsetName = "first")$cluster <- rep(1:2, times = 4)
# the subset's own columns
colData(es, subsetName = "first")
#> DataFrame with 8 rows and 1 column
#>         cluster
#>       <integer>
#> cell1         1
#> cell2         2
#> cell3         1
#> cell4         2
#> cell5         1
#> cell6         2
#> cell7         1
#> cell8         2
# with the main object's columns first
colData(es, subsetName = "first", parentColData = TRUE)
#> DataFrame with 8 rows and 2 columns
#>            sample   cluster
#>       <character> <integer>
#> cell1           A         1
#> cell2           A         2
#> cell3           A         1
#> cell4           A         2
#> cell5           A         1
#> cell6           A         2
#> cell7           A         1
#> cell8           A         2
# the subset's rowData, which has no columns yet
rowData(es, subsetName = "first")
#> DataFrame with 5 rows and 0 columns

Usage

Arguments

Value

See also

Examples