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Things that CRAN wants. (#135)
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‎docs/packages/airr-R/topics.rst

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topics/validate_airr
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topics/load_schema
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topics/Schema-class
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topics/ExampleData

‎docs/packages/airr-R/topics/ExampleData.rst

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ExampleData
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-----------
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**Example AIRR data**
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Description
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~~~~~~~~~~~
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Example data files compliant with the the AIRR Data Representation
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standards.
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Format
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~~~~~~
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``extdata/rearrangement-example.tsv.gz``: Rearrangement TSV file.
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Examples
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~~~~~~~~
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.. code:: r
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# Get path to the rearrangement-example file
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file <- system.file("extdata", "rearrangement-example.tsv.gz", package="airr")
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# Load data file
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df <- read_rearrangement(file)

‎docs/packages/airr-R/topics/load_schema.rst

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.. code:: r
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# Load the rearrangement definition
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# Load the Rearrangement definition
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schema <- load_schema("Rearrangement")
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# Load the Alignment definition
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schema <- load_schema("Alignment")
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See also
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~~~~~~~~
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‎docs/packages/airr-R/topics/read_airr.rst

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.. code:: r
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### Not run:
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# Read a Rearrangement TSV file with default options
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# df <- read_rearrangement("file.tsv")
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# Get path to the rearrangement-example file
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file <- system.file("extdata", "rearrangement-example.tsv.gz", package="airr")
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# Load data file
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df <- read_rearrangement(file)
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See also
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~~~~~~~~

‎docs/packages/airr-R/topics/validate_airr.rst

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.. code:: r
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### Not run:
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# Get path to the rearrangement-example file
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file <- system.file("extdata", "rearrangement-example.tsv.gz", package="airr")
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# Load data file
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df <- read_rearrangement(file)
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# Validate a data.frame against the Rearrangement schema
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# validate_airr(data, schema=RearrangementSchema)
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validate_airr(data, schema=RearrangementSchema)
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*Warning*:Warning: File is missing AIRR mandatory field(s): sequence_id,
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sequence, rev_comp, productive, v_call, d_call, j_call,
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sequence_alignment, germline_alignment, junction, junction_aa, v_cigar,
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d_cigar, j_cigar
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::
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[1] FALSE
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‎docs/packages/airr-R/topics/write_airr.rst

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.. code:: r
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### Not run:
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# Get path to the rearrangement-example file
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file <- system.file("extdata", "rearrangement-example.tsv.gz", package="airr")
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# Load data file
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df <- read_rearrangement(file)
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# Write a Rearrangement data file
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# write_rearrangement(data, "file.tsv")
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outfile <- file.path(tempdir(), "output.tsv")
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write_rearrangement(df, outfile)
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See also
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~~~~~~~~

‎docs/packages/airr-R/vignettes/Usage-Vignette.rst

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library(airr)
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example_data <- file.path("..", "tests", "data-tests", "toy_data.tsv")
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example_data <- system.file("extdata", "rearrangement-example.tsv.gz", package="airr")
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basename(example_data)
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::
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## [1] "toy_data.tsv"
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## [1] "rearrangement-example.tsv.gz"
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.. code:: r
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::
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## # A tibble: 6 x 44
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## rearrangement_id rearrangement_se… sequence_id sequence rev_comp
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## <chr> <chr> <chr> <chr> <lgl>
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## 1 IVKNQEJ01BVGQ6 1 IVKNQEJ01B… GGCCCAGGACTGGTG… TRUE
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## 2 IVKNQEJ01AQVWS 1 IVKNQEJ01A… GGCCCAGGACTGGTG… TRUE
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## 3 IVKNQEJ01AOYFZ 1 IVKNQEJ01A… GGCCCAGGACTGGTG… TRUE
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## 4 IVKNQEJ01EI5S4 1 IVKNQEJ01E… GGCCCAGGACTGGTG… TRUE
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## 5 IVKNQEJ01DGRRI 1 IVKNQEJ01D… GGCCCAGGACTGGTG… TRUE
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## 6 IVKNQEJ01APN5N 1 IVKNQEJ01A… GGCCCAGGACTGGTG… TRUE
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## # ... with 39 more variables: productive <lgl>, sequence_alignment <chr>,
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## # germline_alignment <chr>, v_call <chr>, d_call <chr>, j_call <chr>,
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## # c_call <chr>, junction <chr>, junction_length <int>,
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## # junction_aa <chr>, v_score <dbl>, d_score <dbl>, j_score <dbl>,
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## # c_score <dbl>, v_cigar <chr>, d_cigar <chr>, j_cigar <chr>,
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## # c_cigar <chr>, v_identity <dbl>, v_evalue <dbl>, d_identity <dbl>,
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## # d_evalue <dbl>, j_identity <dbl>, j_evalue <dbl>,
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## # A tibble: 6 x 33
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## sequence_id sequence rev_comp productive stop_codon vj_in_frame v_call
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## <chr> <chr> <lgl> <lgl> <lgl> <lgl> <chr>
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## 1 SRR765688.7… NNNNNNNN… FALSE TRUE FALSE TRUE IGHV2…
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## 2 SRR765688.3… NNNNNNNN… FALSE TRUE FALSE TRUE IGHV5…
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## 3 SRR765688.3… NNNNNNNN… FALSE TRUE FALSE TRUE IGHV7…
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## 4 SRR765688.3… NNNNNNNN… FALSE TRUE FALSE TRUE IGHV7…
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## 5 SRR765688.4… NNNNNNNN… FALSE TRUE FALSE TRUE IGHV7…
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## 6 SRR765688.1… NNNNNNNN… FALSE FALSE TRUE TRUE IGHV2…
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## # ... with 26 more variables: d_call <chr>, j_call <chr>, c_call <chr>,
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## # sequence_alignment <chr>, germline_alignment <chr>, junction <chr>,
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## # junction_aa <chr>, v_cigar <chr>, d_cigar <chr>, j_cigar <chr>,
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## # junction_length <int>, np1_length <int>, np2_length <int>,
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## # v_sequence_start <dbl>, v_sequence_end <int>, v_germline_start <dbl>,
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## # v_germline_end <int>, d_sequence_start <dbl>, d_sequence_end <int>,
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## # d_germline_start <dbl>, d_germline_end <int>, j_sequence_start <dbl>,
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## # j_sequence_end <int>, j_germline_start <dbl>, j_germline_end <int>,
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## # np1_length <int>, np2_length <int>, duplicate_count <int>
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## # duplicate_count <int>
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Writing AIRR formatted files
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----------------------------

‎lang/R/R/Interface.R

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#' See \link{write_airr} for writing AIRR data.
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#'
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#' @examples
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#' \dontrun{
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#' # Read a Rearrangement TSV file with default options
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#' df <- read_rearrangement("file.tsv")
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#' }
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#' # Get path to the rearrangement-example file
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#' file <- system.file("extdata", "rearrangement-example.tsv.gz", package="airr")
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#'
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#' # Load data file
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#' df <- read_rearrangement(file)
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#'
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#' @export
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read_airr <- function(file, base=c("0", "1"), schema=RearrangementSchema, ...) {
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#' \code{FALSE} if not.
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#'
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#' @examples
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#' \dontrun{
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#' # Validate a data.frame against the Rearrangement schema
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#' validate_airr(data, schema=RearrangementSchema)
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#' }
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#' # Get path to the rearrangement-example file
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#' file <- system.file("extdata", "rearrangement-example.tsv.gz", package="airr")
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#'
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#' # Load data file
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#' df <- read_rearrangement(file)
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#'
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#' # Validate a data.frame against the Rearrangement schema
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#' validate_airr(data, schema=RearrangementSchema)
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#'
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#' @export
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validate_airr <- function(data, schema=RearrangementSchema){
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#' See \link{read_airr} for reading to AIRR files.
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#'
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#' @examples
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#' \dontrun{
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#' # Write a Rearrangement data file
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#' write_rearrangement(data, "file.tsv")
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#' }
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#' # Get path to the rearrangement-example file
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#' file <- system.file("extdata", "rearrangement-example.tsv.gz", package="airr")
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#'
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#' # Load data file
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#' df <- read_rearrangement(file)
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#'
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#' # Write a Rearrangement data file
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#' outfile <- file.path(tempdir(), "output.tsv")
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#' write_rearrangement(df, outfile)
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#'
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#' @export
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write_airr <- function(data, file, base=c("0", "1"), schema=RearrangementSchema, ...) {

‎lang/R/R/Schema.R

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#' @seealso See \link{Schema} for the return object.
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#'
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#' @examples
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#' # Load the rearrangement definition
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#' # Load the Rearrangement definition
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#' schema <- load_schema("Rearrangement")
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#'
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#' # Load the Alignment definition
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#' schema <- load_schema("Alignment")
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#'
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#' @export
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load_schema <- function(definition) {
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#### Data ####
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#' Example AIRR data
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#'
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#' Example data files compliant with the the AIRR Data Representation standards.
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#'
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#' @format
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#' \code{extdata/rearrangement-example.tsv.gz}: Rearrangement TSV file.
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#'
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#' @examples
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#' # Get path to the rearrangement-example file
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#' file <- system.file("extdata", "rearrangement-example.tsv.gz", package="airr")
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#'
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#' # Load data file
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#' df <- read_rearrangement(file)
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#'
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#' @name ExampleData
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NULL
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#' @details \code{AlignmentSchema}: AIRR Alignment \code{Schema}.
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#' @rdname Schema-class
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#' @export

‎lang/R/inst/extdata/rearrangement-example.tsv.gz

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‎lang/R/vignettes/Usage-Vignette.Rmd

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```{r read_rearrangement, message=FALSE}
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library(airr)
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example_data <- file.path("..", "tests", "data-tests", "toy_data.tsv")
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example_data <- system.file("extdata", "rearrangement-example.tsv.gz", package="airr")
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basename(example_data)
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airr_rearrangement <- read_rearrangement(example_data, base="0")
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class(airr_rearrangement)

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