airr (version 1.3.0)

read_airr: Read an AIRR TSV

Description

read_airr reads a TSV containing AIRR records.

Usage

read_airr(file, base = c("1", "0"), schema = RearrangementSchema, ...)
read_rearrangement(file, base = c("1", "0"), ...)
read_alignment(file, base = c("1", "0"), ...)

Value

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

Arguments

file

input file path.

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).

schema

Schema object defining the output format.

...

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.

See Also

See Schema for the AIRR schema object definition. See write_airr 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)