Valid annotation values

Source: R/check-annotation-values.R

Checks for and returns the valid annotation valaues in a data frame, Synapse file, or Synapse file view.

valid_annotation_values(x, annotations, ...)

# S3 method for `NULL`
valid_annotation_values(x, annotations, ...)

# S3 method for synapseclient.entity.File
valid_annotation_values(x, annotations, syn, ...)

# S3 method for data.frame
valid_annotation_values(x, annotations, ...)

# S3 method for synapseclient.table.CsvFileTable
valid_annotation_values(x, annotations, ...)

Arguments

x

An object to check.
annotations

A data frame of annotation definitions. Must contain at least three columns: key, value, and columnType.
...

Additional options to check_values()
syn

Synapse client object

Value

A named list of valid annotation values.

Methods (by class)

  • NULL: Return NULL

  • synapseclient.entity.File: Valid annotation values on a Synapse file

  • data.frame: Valid annotation values in a data frame

  • synapseclient.table.CsvFileTable: Valid annotation values in a Synapse table

Examples

annots <- data.frame(
  key = c("assay", "fileFormat", "fileFormat", "fileFormat", "species"),
  value = c("rnaSeq", "fastq", "txt", "csv", "Human"),
  columnType = c("STRING", "STRING", "STRING", "STRING", "STRING")
)
dat1 <- data.frame(assay = "not a valid assay")
dat2 <- data.frame(assay = "rnaSeq")
valid_annotation_values(dat1, annots)

#> named list()
valid_annotation_values(dat2, annots)

#> $assay
#> [1] "rnaSeq"
#>