run_last: Wrapper to run last from an R session

In almeidasilvaf/syntenet: Inference And Analysis Of Synteny Networks

Wrapper to run last from an R session

Description

Wrapper to run last from an R session

Usage

run_last(
  seq = NULL,
  verbose = FALSE,
  outdir = tempdir(),
  threads = 1,
  compare = "all",
  lastD = 1e+06,
  ...
)

Arguments

seq	A processed list of AAStringSet objects as returned by process_input().
verbose	Logical indicating if progress messages should be printed. Default: FALSE.
outdir	Output directory for last results. By default, output files are saved to a temporary directory.
threads	Number of threads to use. Default: 1.
compare	Character scalar indicating which comparisons should be made when running last. 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.
lastD	last option D: query letters per random alignment. Default: 1e6.
...	Any additional arguments to lastal.

Value

A list of data frames containing last'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(last_is_installed()) {
    last_results <- run_last(seq)
}

almeidasilvaf/syntenet documentation built on Oct. 12, 2024, 5:51 p.m.