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,
  param
)

Arguments

results_table	data.frame containing the MetaScope results.
bam_file	Rsamtools::bamFile instance for the given sample.
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 file.path(directory_here, "X78256") with extension omitted.
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 metascope_id are stored.
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	BiocParallel param for parallelization.

Value

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

compbiomed/MetaScope documentation built on Nov. 30, 2024, 4:35 p.m.