valid_annotation_values: Valid annotation values

In Sage-Bionetworks/dccvalidator: Metadata Validation for Data Coordinating Centers

Valid annotation values

Description

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

Usage

valid_annotation_values(x, annotations, ...)

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

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

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

## S3 method for class '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)
valid_annotation_values(dat2, annots)

Sage-Bionetworks/dccvalidator documentation built on May 7, 2022, 10:32 a.m.