read_airr {airr}R Documentation

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"), ...)

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.

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_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)


[Package airr version 1.3.0 Index]