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PlySummarizedExperiment Methods

Source: R/plyxp-class.R
PlySummarizedExperiment-methods.Rd

Methods from SummarizedExperiment package re-implemented for PlySummarizedExperiment.

Usage

se(x)

# S4 method for class 'PlySummarizedExperiment'
se(x)

se(x) <- value

# S4 method for class 'PlySummarizedExperiment'
se(x) <- value

# S4 method for class 'PlySummarizedExperiment'
assays(x, withDimnames = TRUE, ...)

# S4 method for class 'PlySummarizedExperiment,list'
assays(x, withDimnames = TRUE, ...) <- value

# S4 method for class 'PlySummarizedExperiment,SimpleList'
assays(x, withDimnames = TRUE, ...) <- value

# S4 method for class 'PlySummarizedExperiment,missing'
assay(x, i, withDimnames = TRUE, ...)

# S4 method for class 'PlySummarizedExperiment,numeric'
assay(x, i, withDimnames = TRUE, ...)

# S4 method for class 'PlySummarizedExperiment,character'
assay(x, i, withDimnames = TRUE, ...)

# S4 method for class 'PlySummarizedExperiment,missing'
assay(x, i, withDimnames = TRUE, ...) <- value

# S4 method for class 'PlySummarizedExperiment,numeric'
assay(x, i, withDimnames = TRUE, ...) <- value

# S4 method for class 'PlySummarizedExperiment,character'
assay(x, i, withDimnames = TRUE, ...) <- value

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

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

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

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

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

Arguments

x

PlySummarizedExperiment object

value

replacement value

withDimnames

logical

...

additional arguments

i

character or numeric index

use.names

logical

Value

Replacement functions return a PlySummarizedExperiment object. Other functions will return the same object as the method from SummarizedExperiment.

Functions

  • se(PlySummarizedExperiment): get the se slot of the PlySummarizedExperiment object

  • se(x) <- value: set the se slot of the PlySummarizedExperiment object

  • se(PlySummarizedExperiment) <- value: set the se slot of the PlySummarizedExperiment object

  • assays(PlySummarizedExperiment): get the assays o the PlySummarizedExperiment object

  • assays(x = PlySummarizedExperiment) <- value: set the assays of the PlySummarizedExperiment object

  • assays(x = PlySummarizedExperiment) <- value: set the assays of the PlySummarizedExperiment object

  • assay(x = PlySummarizedExperiment, i = missing): get the first assay of the PlySummarizedExperiment object

  • assay(x = PlySummarizedExperiment, i = numeric): get assay from a PlySummarizedExperiment object

  • assay(x = PlySummarizedExperiment, i = character): get assay from a PlySummarizedExperiment object

  • assay(x = PlySummarizedExperiment, i = missing) <- value: set assay in a PlySummarizedExperiment object

  • assay(x = PlySummarizedExperiment, i = numeric) <- value: set assay in a PlySummarizedExperiment object

  • assay(x = PlySummarizedExperiment, i = character) <- value: set assay in a PlySummarizedExperiment object

  • rowData(PlySummarizedExperiment): get rowData in a PlySummarizedExperiment object

  • rowData(PlySummarizedExperiment) <- value: set rowData in a PlySummarizedExperiment object

  • colData(PlySummarizedExperiment): get colData in a PlySummarizedExperiment object

  • colData(x = PlySummarizedExperiment) <- value: set colData in a PlySummarizedExperiment object

Examples

assays(se_simple)
#> List of length 2
#> names(2): counts logcounts
rowData(se_simple)
#> DataFrame with 5 rows and 3 columns
#>              gene    length   direction
#>       <character> <integer> <character>
#> row_1          g1         1           -
#> row_2          g2        24           +
#> row_3          g3        60           +
#> row_4          g4        39           -
#> row_5          g5        37           +
colData(se_simple)
#> DataFrame with 4 rows and 2 columns
#>            sample   condition
#>       <character> <character>
#> col_1          s1       cntrl
#> col_2          s2       cntrl
#> col_3          s3        drug
#> col_4          s4        drug