Sanitize sample data

Drop any columns defined in denylist, and ensure character columns containing any duplicate values are automatically coerced to factor.

Usage

sanitizeSampleData(object)

Arguments

object

DFrame (recommended) or data.frame (legacy). Note that legacy data.frame support will be removed in a future update.

Value

DFrame.

Note

Updated 2023-04-27.

Denylist

Here's the current column denylist:

• interestingGroups.

• sampleId.

Examples

data(RangedSummarizedExperiment, package = "AcidTest")
rse <- RangedSummarizedExperiment

## SummarizedExperiment ====
from <- sampleData(rse)
print(from)
#> DataFrame with 12 rows and 3 columns
#>          condition sampleName interestingGroups
#>           <factor>   <factor>          <factor>
#> sample01         A   sample01                 A
#> sample02         A   sample02                 A
#> sample03         A   sample03                 A
#> sample04         A   sample04                 A
#> sample05         A   sample05                 A
#> ...            ...        ...               ...
#> sample08         B   sample08                 B
#> sample09         B   sample09                 B
#> sample10         B   sample10                 B
#> sample11         B   sample11                 B
#> sample12         B   sample12                 B
to <- sanitizeSampleData(from)
all(vapply(to, is.factor, logical(1L)))
#> [1] TRUE
print(to)
#> DataFrame with 12 rows and 2 columns
#>          condition sampleName
#>           <factor>   <factor>
#> sample01         A   sample01
#> sample02         A   sample02
#> sample03         A   sample03
#> sample04         A   sample04
#> sample05         A   sample05
#> ...            ...        ...
#> sample08         B   sample08
#> sample09         B   sample09
#> sample10         B   sample10
#> sample11         B   sample11
#> sample12         B   sample12