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New Biocmask

Source: R/biocmask.R
new_biocmask_manager.Rd

Create a biocmask for an object

Usage

new_biocmask_manager(obj, ...)

# S3 method for class 'SummarizedExperiment'
new_biocmask_manager(obj, ...)

Arguments

obj

Dispatch Object

...

Not used

Value

a biocmask_manager R6 class object

See also

BiocmaskManager

Examples

 
manager <- new_biocmask_manager(se_simple)
manager$ctx
#> [1] "assays"
q <- biocmask_quos(counts_1 = counts + 1,
                   cols(is_drug = condition=="drug"),
                   .ctx_default = "assays",
                   .ctx_opt = c("rows", "cols"))
manager$eval(q[[1]])
manager$results()
#> $assays
#> $assays$counts_1
#>      [,1] [,2] [,3] [,4]
#> [1,]   15    9    8   10
#> [2,]   20    3    2    5
#> [3,]   17    7   16   21
#> [4,]   12   18   11    4
#> [5,]   19   14   13    6
#> 
#> 
#> $rows
#> named list()
#> 
#> $cols
#> named list()
#> 
#evaluating second quo without switching contexts will error
manager$eval(q[[2]]) |> try()
#> Error : object 'condition' not found
manager$ctx <- "cols"
manager$ctx
#> [1] "cols"
manager$eval(q[[2]])
manager$results()
#> $assays
#> $assays$counts_1
#>      [,1] [,2] [,3] [,4]
#> [1,]   15    9    8   10
#> [2,]   20    3    2    5
#> [3,]   17    7   16   21
#> [4,]   12   18   11    4
#> [5,]   19   14   13    6
#> 
#> 
#> $rows
#> named list()
#> 
#> $cols
#> $cols$is_drug
#> [1] FALSE FALSE  TRUE  TRUE
#> 
#>