read_tabular {airr}

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)