validate_airr#
Validate an AIRR Data Model nested list representation
Description#
validate_airr
validates the fields in a named nested list
representation of the AIRR Data Model. Typically, generating by reading
of JSON or YAML formatted AIRR files.
Usage#
validate_airr(data, model = TRUE, each = FALSE)
Arguments#
- data
list
containing records of an AIRR Data Model objected imported from a YAML or JSON representation.- model
if
TRUE
validate only AIRR DataFile defined objects. IfFALSE
attempt validation of all objects indata
.- each
if
TRUE
return a logical vector with results for each object indata
instead of a singleTRUE
orFALSE
value.
Value#
Returns TRUE
if the input data
is compliant with AIRR standards
and FALSE
if not. If each=TRUE
is set, then a vector with
results for each each object in data
is returned instead.
Examples#
# Get path to the rearrangement-example file
f1 <- system.file("extdata", "repertoire-example.yaml", package="airr")
f2 <- system.file("extdata", "germline-example.json", package="airr")
# Load data file
repertoire <- read_airr(f1)
germline <- read_airr(f2)
# Validate a single record
validate_airr(repertoire)
[1] TRUE
# Return validation for individual objects
validate_airr(germline, each=TRUE)
GenotypeSet GermlineSet
TRUE TRUE
See also#
See Schema for the AIRR schema definitions. See read_airr for loading AIRR Data Models from a file. See write_airr for writing AIRR Data Models to a file.