Check annotation values

Source: R/check-annotation-values.R

Checks that all annotation values are valid. It does not report on values for invalid keys; see check_annotation_keys().

check_annotation_values(x, annotations, ...)

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

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

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

# S3 method for synapseclient.table.CsvFileTable
check_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 condition object indicating whether all annotation values are valid. Invalid annotation values are included as data within the object.

Details

If the allowable annotation values are an enumerated list, check_annotation_values() compares the values in the data to the values in this list. If there is no enumerated list of values and the annotation definition merely specifies a required type, then the values are checked against that type, with values that are coercible to the correct type treated as valid (see can_coerce()).

Methods (by class)

  • NULL: Return NULL

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

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

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

See also

valid_annotation_values(), can_coerce()

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")
check_annotation_values(dat1, annots)

#> <error/check_fail>
#> Some annotation values are invalid
check_annotation_values(dat2, annots)

#> <check_pass: All annotation values are valid>
if (FALSE) {
syn <- synapse$Synapse()
syn$login()

annots <- get_synapse_annotations(syn = syn)
my_file <- syn$get("syn11931757", downloadFile = FALSE)
check_annotation_values(my_file, annots)

dat <- data.frame(
  non_annotation = 5:7,
  assay = c("rnaSeq", "foo", "bar"),
  stringsAsFactors = FALSE
)
check_annotation_values(dat, annots)

fv <- synTableQuery("SELECT * FROM syn17020234")
check_annotation_values(fv, annots)

# If you don't specify an annotations data frame, these functions will
# download annotations automatically using `get_synapse_annotations()` (must
# be logged in to Synapse)
my_file <- syn$get("syn11931757", downloadFile = FALSE)
check_annotation_values(my_file, syn = syn)

# It is possible to allowlist certain certain values, or all values for
# certain keys:
check_annotation_values(dat, allowlist_keys = "assay", syn = syn)

check_annotation_values(
  dat,
  allowlist_values = list(assay = c("foo")),
  syn = syn
)
}