blastn_single_result: blastn_single_result

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

blastn_single_result

Description

blastn_single_result

Usage

blastn_single_result(
  results_table,
  bam_file,
  which_result,
  num_reads = 100,
  hit_list = 10,
  num_threads = 1,
  db_path,
  quiet,
  accessions_path,
  bam_seqs,
  out_path,
  sample_name,
  fasta_dir = NULL
)

Arguments

results_table	A dataframe of the Metascope results
bam_file	A sorted bam file and index file, loaded with Rsamtools::bamFile
which_result	Index in results_table for which result to Blast search
num_reads	Number of reads to blast per result
hit_list	Number of how many blast results to fetch per read
num_threads	Number of threads if multithreading
db_path	Blast database path
quiet	Logical, whether to print out more informative messages. Default is FALSE.
accessions_path	Directory where accession files for blast are stored.
bam_seqs	A list of the sequence IDs from the bam file
out_path	Path to output results.
sample_name	Character string, sample name for output files.
fasta_dir	Path to where fasta files are stored.

Value

Returns a dataframe of blast results for a metascope result

compbiomed/MetaScope documentation built on June 24, 2024, 9 a.m.