write_tabular {airr}

Write an AIRR tabular data

Description

write_tabular writes a TSV containing AIRR tabular records.

Usage

write_tabular(data, file, schema, base = c("1", "0"), ...)

write_rearrangement(data, file, base = c("1", "0"), ...)

write_alignment(data, file, base = c("1", "0"), ...)

Arguments

data

data.frame of Rearrangement data.

file

output file name.

schema

Schema object defining the output format.

base

starting index for positional fields in the output file. Fields in the input data are assumed to be 1-based closed-intervals (R style). If "1", then these fields will not be modified. If "0", then fields ending in _start and _end will be converted to 0-based half-open intervals (python style) in the output file.

...

additional arguments to pass to write_delim.

Details

write_rearrangement writes a data.frame containing AIRR Rearrangement data to TSV.

write_alignment writes a data.frame containing AIRR Alignment data to TSV.

See Also

See Schema for the AIRR schema object definition. See read_tabular for reading to AIRR files.

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)

# Write a Rearrangement data file
outfile <- file.path(tempdir(), "output.tsv")
write_tabular(df, outfile, schema=RearrangementSchema)