read_tabular
Contents
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)
See also#
See Schema for the AIRR schema object definition. See write_tabular for writing AIRR data.