airr (version 1.1.0)

read_airr: Read an AIRR TSV

Description

read_airr reads a TSV containing AIRR records.

Usage

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

Arguments

file

input file path.

base

starting index for positional fields in the input file. 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). If "1", then these fields will not be modified.

schema

Schema object defining the output format.

...

additional arguments to pass to read_delim.

Value

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

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

# NOT RUN {
# Get path to the rearrangement-example file
file <- system.file("extdata", "rearrangement-example.tsv.gz", package="airr")

# Load data file
df <- read_rearrangement(file)

# }