rBLAST_single_result: rBLAST_single_result

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

rBLAST_single_result

Description

rBLAST_single_result

Usage

rBLAST_single_result(
  results_table,
  bam_file,
  which_result,
  num_reads = 100,
  hit_list = 10,
  num_threads = 1,
  db_path,
  quiet = quiet,
  NCBI_key = NULL,
  bam_seqs
)

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.
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.
bam_seqs	A list of the sequence IDs from the bam file

Value

Returns a dataframe of blast results for a metascope result

compbiomed/MetaScope documentation built on April 1, 2024, 5:35 p.m.