makeSignatures Creates signatures for a list of bug signatures from
a tidy data.frame imported through the importBugphyzz function. Please
run browseVignettes("bugphyz") for detailed examples.
makeSignatures(
dat,
taxIdType = c("NCBI_ID", "Taxon_name"),
taxLevel = c("mixed", "superkingdom", "phylum", "class", "order", "family", "genus",
"species", "strain"),
evidence = c("exp", "igc", "tas", "nas", "tax", "asr"),
frequency = c("always", "usually", "sometimes", "unknown"),
minSize = 10,
min = NULL,
max = NULL
)A data.frame.
A character string. Valid options: NCBI_ID, Taxon_name.
A character vector. Taxonomic rank. Valid options: superkingdom, kingdom, phylum, class, order, family, genus, species, strain. They can be combined. "mixed" is equivalent to select all valid ranks.
A character vector. Valid options: exp, igc, nas, tas, tax, asr. They can be combined. Default is all.
A character vector. Valid options: always, usually, sometimes, rarely, unknown. They can be combined. By default, "rarely" is excluded.
Minimum number of bugs in a signature. Default is 10.
Minimum value (inclusive). Only for numeric attributes. Default is NULL.
Maximum value (inclusive). Only for numeric attributes. Default is NULL.
A list of character vectors with scientific names or taxids.
bp <- importBugphyzz()
#> Using data downloaded on 2024-08-26 15:06:32.
sigs <- purrr::map(bp, makeSignatures)
sigs <- purrr::list_flatten(sigs, name_spec = "{inner}")