read_airr

Read an AIRR Data Model file in YAML or JSON format

Description

read_airr loads a YAML or JSON file containing AIRR Data Model records.

Usage

read_airr(
file,
format = c("auto", "yaml", "json"),
validate = TRUE,
model = TRUE
)

Arguments

file

path to the input file.

format

format of the input file. Must be one of "auto", "yaml", or "json". If "auto" (default), the format will be detected from the file extension.

validate

run schema validation if TRUE.

model

if TRUE validate only AIRR DataFile defined objects. If FALSE attempt validation of all objects in data. Ignored if validate=FALSE

Value

A named nested list contained in the AIRR Data Model with the top-level names reflecting the individual AIRR objects.

Examples

# Get path to the Reportoire and GermlineSet example files
f1 <- system.file("extdata", "repertoire-example.yaml", package="airr")
f2 <- system.file("extdata", "germline-example.json", package="airr")

# Load data files
repertoire <- read_airr(f1)
germline <- read_airr(f2)

See also

See Schema for the AIRR schema definition objects. See write_airr for writing AIRR Data Model records in YAML or JSON format.