Wrapper to run DIAMOND from an R session

Wrapper to run DIAMOND from an R session

Usage

run_diamond(
  seq = NULL,
  top_hits = 5,
  verbose = FALSE,
  outdir = tempdir(),
  threads = NULL,
  compare = "all",
  ...
)

Arguments

seq

A processed list of AAStringSet objects as returned by process_input().

top_hits

Number of top hits to keep in DIAMOND search. Default: 5.

verbose

Logical indicating if progress messages should be printed. Default: FALSE.

outdir

Output directory for DIAMOND results. By default, output files are saved to a temporary directory.

threads

Number of threads to use. Default: let DIAMOND auto-detect and use all available virtual cores on the machine.

compare

Character scalar indicating which comparisons should be made when running DIAMOND. Possible modes are "all" (all-vs-all comparisons), "intraspecies" (intraspecies comparisons only), or "interspecies" (interspecies comparisons only). Alternatively, users can pass a 2-column data frame as input with the names of species to be compared.

...

Any additional arguments to diamond blastp.

Value

A list of data frames containing DIAMOND's tabular output for each pairwise combination of species. For n species, the list length will be \(n^2\).

Examples

data(proteomes)
data(annotation)
seq <- process_input(proteomes, annotation)$seq[1:2]
if(diamond_is_installed()) {
    diamond_results <- run_diamond(seq)
}