rBlast_results
Usage
blastn_results(
results_table,
bam_file,
num_results = 10,
num_reads_per_result = 100,
hit_list = 10,
num_threads = 1,
db_path,
out_path,
sample_name = NULL,
quiet = quiet,
accessions_path,
fasta_dir = NULL,
NCBI_key = NULL
)Arguments
- results_table
A data.frame of the Metascope results
- bam_file
A sorted bam file and index file, loaded with Rsamtools::bamFile
- num_results
A number indicating number of Metascope results to blast
- num_reads_per_result
A number indicating number of reads to blast per result
- hit_list
A number of how many blast results to fetch for each read
- num_threads
Number of threads if multithreading
- db_path
Blast database path
- out_path
Output directory to save csv files, including base name of files
- sample_name
Character string, sample name for output files.
- quiet
Logical, whether to print out more informative messages. Default is FALSE.
- accessions_path
Directory where accession files for blast are stored.
- fasta_dir
inc.
- NCBI_key
(character) NCBI Entrez API key. optional. See taxize::use_entrez(). Due to the high number of requests made to NCBI, this function will be less prone to errors if you obtain an NCBI key.