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## -----------------------------------------------------------------------------
# Imports
library(airr)
library(tibble)
# Read Rearrangement example file
f1 <- system.file("extdata", "rearrangement-example.tsv.gz", package="airr")
rearrangement <- read_rearrangement(f1)
glimpse(rearrangement)
## -----------------------------------------------------------------------------
# Read Repertoire example file
f2 <- system.file("extdata", "repertoire-example.yaml", package="airr")
repertoire <- read_airr(f2)
glimpse(repertoire)
# Read GermlineSet example file
f3 <- system.file("extdata", "germline-example.json", package="airr")
germline <- read_airr(f3)
glimpse(germline)
## -----------------------------------------------------------------------------
x1 <- file.path(tempdir(), "airr_out.tsv")
write_rearrangement(rearrangement, x1)
## -----------------------------------------------------------------------------
x2 <- file.path(tempdir(), "airr_repertoire_out.yaml")
write_airr(repertoire, x2, format="yaml")
x3 <- file.path(tempdir(), "airr_germline_out.json")
write_airr(germline, x3, format="json")
## -----------------------------------------------------------------------------
# Validate Rearrangement data.frame
validate_rearrangement(rearrangement)
# Validate an AIRR Data Model
validate_airr(repertoire)
# Validate AIRR Data Model records individual
validate_airr(germline, each=TRUE)
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