read_tabular#

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.

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.

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)

read_tabular

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