blast_to_wide: Convert BLAST results to a wide table

In vmikk/metagMisc: Miscellaneous functions for metagenomic analysis

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.