View source: R/03_similarity_searches.R
run_diamond | R Documentation |
Wrapper to run DIAMOND from an R session
run_diamond(
seq = NULL,
top_hits = 5,
verbose = FALSE,
outdir = tempdir(),
threads = NULL,
compare = "all",
...
)
seq |
A processed list of AAStringSet objects
as returned by |
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 |
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
.
data(proteomes)
data(annotation)
seq <- process_input(proteomes, annotation)$seq[1:2]
if(diamond_is_installed()) {
diamond_results <- run_diamond(seq)
}
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