Type: Package
Version: 1.5.0
Date: 2023-08-29
Title: AIRR Data Representation Reference Library
Description: Schema definitions and read, write and validation tools for data formatted in accordance with the AIRR Data Representation schemas defined by the AIRR Community http://docs.airr-community.org.
License: CC BY 4.0
URL: http://docs.airr-community.org
BugReports: https://github.com/airr-community/airr-standards/issues
BuildVignettes: true
VignetteBuilder: knitr
Encoding: UTF-8
Depends: R (≥ 3.1.2)
Imports: jsonlite, methods, readr, stats, stringi, tools, yaml
Suggests: knitr, rmarkdown, tibble, testthat
RoxygenNote: 7.2.3
NeedsCompilation: no
Packaged: 2023-08-29 18:26:34 UTC; vandej27
Author: Jason Vander Heiden [aut, cre], Susanna Marquez [aut], Scott Christley [aut], Katharina Imkeller [aut], Ulrik Stervbo [aut], AIRR Community [cph]
Maintainer: Jason Vander Heiden <jason.vanderheiden@gmail.com>
Repository: CRAN
Date/Publication: 2023-08-29 18:50:02 UTC

Example AIRR data

Description

Example data files compliant with the the AIRR Data Representation standards.

Format

Examples

# Load Rearrangement example
file <- system.file("extdata", "rearrangement-example.tsv.gz", package="airr")
rearrangement <- read_rearrangement(file)

# Load Repertoire example
file <- system.file("extdata", "repertoire-example.yaml", package="airr")
repertoire <- read_airr(file)

# Load GermlineSet and GenotypeSet examples
file <- system.file("extdata", "germline-example.json", package="airr")
germline <- read_airr(file)

S4 class defining an AIRR standard schema

Description

Schema defines a common data structure for AIRR Data Representation standards.

Usage

## S4 method for signature 'Schema'
names(x)

## S4 method for signature 'Schema,character'
x[i]

## S4 method for signature 'Schema'
x$name

InfoSchema

DataFileSchema

AlignmentSchema

RearrangementSchema

RepertoireSchema

GermlineSetSchema

GenotypeSetSchema

AIRRSchema

Arguments

x

Schema object.

i

field name.

name

field name.

Format

A Schema object.

An object of class Schema of length 1.

An object of class Schema of length 1.

An object of class Schema of length 1.

An object of class Schema of length 1.

An object of class Schema of length 1.

An object of class Schema of length 1.

An object of class Schema of length 1.

An object of class list of length 26.

Details

The following predefined Schema objects are defined:

InfoSchema: AIRR Info Schema.

DataFileSchema: AIRR DataFile Schema.

AlignmentSchema: AIRR Alignment Schema.

RearrangementSchema: AIRR Rearrangement Schema.

RepertoireSchema: AIRR Repertoire Schema.

GermlineSetSchema: AIRR GermlineSet Schema.

GenotypeSetSchema: AIRR GenotypeSet Schema.

AIRRSchema: named list containing all non-experimental AIRR Schema objects.

Slots

definition

name of the schema definition.

required

character vector of required fields.

optional

character vector of non-required fields.

properties

list of field definitions.

info

list schema information.

See Also

See load_schema for loading a Schema from the definition set.

Load a schema definition

Description

load_schema loads an AIRR object definition from the internal definition set.

Usage

load_schema(definition)

Arguments

definition

name of the schema definition.

Details

Valid definitions include:

Value

A Schema object for the definition.

See Also

See Schema for the return object.

Examples

# Load the Rearrangement definition
schema <- load_schema("Rearrangement")

# Load the Repertoire definition
schema <- load_schema("Repertoire")

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.

See Also

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

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)

Read AIRR tabular data

Description

read_tabular reads a tab-delimited (TSV) file containing tabular AIRR records.

Usage

read_tabular(file, schema, base = c("1", "0"), aux_types = NULL, ...)

read_rearrangement(file, base = c("1", "0"), ...)

read_alignment(file, base = c("1", "0"), ...)

Arguments

file

input file path.

schema

Schema object defining the output format.

base

starting index for positional fields in the input file. If "1", then these fields will not be modified. If "0", then fields ending in "_start" and "_end" are 0-based half-open intervals (python style) in the input file and will be converted to 1-based closed-intervals (R style).

aux_types

named vector or list giving the type for fields that are not defined in schema. The field name is the name, the value the type, denoted by one of "c" (character), "l" (logical), "i" (integer), "d" (double), or "n" (numeric).

...

additional arguments to pass to read_delim.

Details

read_rearrangement reads an AIRR TSV containing Rearrangement data.

read_alignment reads an AIRR TSV containing Alignment data.

Value

A data.frame of the TSV file with appropriate type and position conversion for fields defined in the specification.

See Also

See Schema for the AIRR schema object definition. See write_tabular for writing AIRR data.

Examples

# Get path to the rearrangement-example file
file <- system.file("extdata", "rearrangement-example.tsv.gz", package="airr")

# Load data file
df <- read_rearrangement(file)

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. If FALSE attempt validation of all objects in data.

each

if TRUE return a logical vector with results for each object in data instead of a single TRUE or FALSE 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.

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.

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)

# Return validation for individual objects
validate_airr(germline, each=TRUE)

Validate tabular AIRR data

Description

validate_tabular validates compliance of the contents of a data.frame to the AIRR standards.

Usage

validate_tabular(data, schema)

validate_rearrangement(data)

Arguments

data

data.frame of tabular data to validate.

schema

Schema object defining the data standard of the table.

Details

validate_rearrangement validates the standards compliance of AIRR Rearrangement data stored in a data.frame

Value

Returns TRUE if the input data is compliant and FALSE if not.

Examples

# Get path to the rearrangement-example file
file <- system.file("extdata", "rearrangement-example.tsv.gz", package="airr")

# Load data file
df <- read_rearrangement(file)

# Validate a data.frame against the Rearrangement schema
validate_rearrangement(df)

Write AIRR Data Model records to YAML or JSON files

Description

write_airr writes a YAML or JSON file containing AIRR Data Model records.

Usage

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

Arguments

data

list containing AIRR Model Records.

file

output file name.

format

format of the output 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 prior to write if TRUE.

model

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

See Also

See Schema for the AIRR schema definition objects. See read_airr for reading to AIRR Data Model files.

Examples

# Get path to the repertoire-example file
file <- system.file("extdata", "repertoire-example.yaml", package="airr")

# Load data file
repertoire <- read_airr(file)

# Write a Rearrangement data file
outfile <- file.path(tempdir(), "output.yaml")
write_airr(repertoire, outfile)

Write an AIRR tabular data

Description

write_tabular writes a TSV containing AIRR tabular records.

Usage

write_tabular(data, file, schema, base = c("1", "0"), ...)

write_rearrangement(data, file, base = c("1", "0"), ...)

write_alignment(data, file, base = c("1", "0"), ...)

Arguments

data

data.frame of Rearrangement data.

file

output file name.

schema

Schema object defining the output format.

base

starting index for positional fields in the output file. Fields in the input data are assumed to be 1-based closed-intervals (R style). If "1", then these fields will not be modified. If "0", then fields ending in _start and _end will be converted to 0-based half-open intervals (python style) in the output file.

...

additional arguments to pass to write_delim.

Details

write_rearrangement writes a data.frame containing AIRR Rearrangement data to TSV.

write_alignment writes a data.frame containing AIRR Alignment data to TSV.

See Also

See Schema for the AIRR schema object definition. See read_tabular for reading to AIRR files.

Examples

# Get path to the rearrangement-example file
file <- system.file("extdata", "rearrangement-example.tsv.gz", package="airr")

# Load data file
df <- read_rearrangement(file)

# Write a Rearrangement data file
outfile <- file.path(tempdir(), "output.tsv")
write_tabular(df, outfile, schema=RearrangementSchema)