View source: R/metascope_blast.R
blastn_results | R Documentation |
rBlast_results
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,
param
)
results_table |
data.frame containing the MetaScope results. |
bam_file |
|
num_results |
Integer; maximum number of Metascope results to BLAST. Default is 10. |
num_reads_per_result |
Integer; number of reads to BLAST per result. Default is 100. |
hit_list |
Integer; how many BLAST results to fetch for each read. Default is 10. |
num_threads |
Integer; how many threads to use if multithreading. Default is 1. |
db_path |
Character string; filepath for the location of the pre-installed BLAST database. |
out_path |
Character string; Output directory to save CSV output files,
including base name of files. For example, given a sample "X78256",
filepath would be |
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 |
Character string; Directory where fastas from
|
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. |
param |
|
Creates and exports num_results number of csv files with blast results from local blast
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