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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