blastn_results: rBlast_results

In compbiomed/MetaScope: Tools and functions for preprocessing 16S and metagenomic sequencing microbiome data

rBlast_results

Description

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.

Value

Creates and exports num_results number of csv files with blast results from local blast

compbiomed/MetaScope documentation built on Nov. 5, 2024, 9:25 p.m.