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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