View source: R/metascope_blast.R
blastn_single_result | R Documentation |
blastn_single_result
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
)
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. |
Returns a dataframe of blast results for a metascope result
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