blast_reassignment: Reassign reads from MetaScope BLASTn alignment

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

Reassign reads from MetaScope BLASTn alignment

Description

Using the output from metascope_blast(), the blast_reassignment() function takes the results and alters the original metascope_id() output to reassign reads that were invalidated by the BLAST findings. Currently, the implementation of this function only reassigns reads to a taxon that was already found in the sample at a higher abundance.

Usage

blast_reassignment(
  metascope_blast_path,
  species_threshold,
  num_hits,
  blast_tmp_dir,
  out_dir,
  sample_name
)

Arguments

metascope_blast_path	Character string. The filepath to a metascope_blast CSV output file.
species_threshold	Numeric. A number between 0 and 1 indicating the minimum proportion of reads needed for a taxon to be considered validated from the BLAST results. Default is 0.2, or 20%.
num_hits	Integer. The number of hits for which to assess validation. Default is 10, i.e., only the top 10 taxa will be assessed.
blast_tmp_dir	Character string. Filepath of the directory where BLAST results were output from the metascope_blast function. Referencing the arguments from metascope_blast, this would be file.path(tmp_dir, "blast")
out_dir	Character string, path to output directory.
sample_name	Character string, sample name for output files.

Value

Returns a data.frame with the reassigned taxa and read counts.

compbiomed/MetaScope documentation built on Nov. 20, 2024, 8 p.m.