run_diamond: Wrapper to run DIAMOND from an R session

In almeidasilvaf/syntenet: Inference And Analysis Of Synteny Networks

Wrapper to run DIAMOND from an R session

Description

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)
}

almeidasilvaf/syntenet documentation built on Dec. 23, 2024, 6:26 a.m.