read_diamond: Import DIAMOND2 output file

In drostlab/rdiamond: Seamless Integration of DIAMOND2 Sequence Searches in R

Import DIAMOND2 output file

Description

When performing BLAST searches with the blast_*() functions, the corresponding BLAST output file can be imported into the current R session using this function. All output formats given by BLAST are supported (see e.g. description for details).

Usage

read_diamond(file, out_format, use_arrow_duckdb_connection = FALSE)

Arguments

file	path to BLAST output file.
out_format	a character string specifying the output format of the BLAST output that shall be imported. Available options are: out_format = "xml" : XML out_format = "csv" : Comma-separated values
use_arrow_duckdb_connection	shall DIAMOND2 hit output table be transformed to an in-process (big data disk-processing) arrow connection to DuckDB? This is useful when the DIAMOND2 output table to too large to fit into memory. Default is use_arrow_duckdb_connection = FALSE.

Author(s)

Hajk-Georg Drost

See Also

diamond_protein_to_protein

drostlab/rdiamond documentation built on Oct. 23, 2023, 1 p.m.