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 thefile
extension.- validate
run schema validation if
TRUE
.- model
if
TRUE
validate only AIRR DataFile defined objects. IfFALSE
attempt validation of all objects indata
. Ignored ifvalidate=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.