blast_to_wide: Convert BLAST results to a wide table

View source: R/blast_to_wide.R

blast_to_wideR Documentation

Convert BLAST results to a wide table

Description

Convert BLAST results to a wide table

Usage

blast_to_wide(
  blst,
  max_hits = 10,
  taxonomy = NULL,
  seqs = NULL,
  refs = NULL,
  add_coverage = TRUE,
  verbose = TRUE
)

Arguments

blst

Data.table with blast hits (in long format, from m8 file)

max_hits

Number of targets to preserve in a table

taxonomy
  • "NA", no taxonomy should be added to the table

  • "NULL", use default tax ranks (Kingdom - Species)

  • "custom character vector" with column names that contain taxonomy information

seqs

Query sequences (XStringSet object from Biostrings package)

refs

Target sequences (XStringSet object from Biostrings package)

add_coverage

Logical, add query coverage to the output (default, TRUE)

verbose

Logical, produce more screen output (default, TRUE)

Details

For each query, matches should be sorted in the desired order (e.g., by BitScore or E-Value).

Value

data.table


vmikk/metagMisc documentation built on June 20, 2024, 7:20 a.m.