add_patterns | R Documentation |
This function determines unique orthogroup presence/absence patterns in genomes and adds this information to a tidygenomes object.
add_patterns(tg)
tg |
A tidygenomes object |
The following will be added to the tidygenomes object:
A variable pattern
in the orthogroups table, with for each orthogroup its
presence/absence pattern.
A table components
, listing the genomes defining each presence/absence
pattern.
A table patterns
with for each pattern, the number of orthogroups that
follow it.
A tidygenomes object
genes <- data.frame(
gene = c("gene A", "gene B", "gene C"),
genome = c("genome 1", "genome 1", "genome 2"),
orthogroup = c("og alpha", "og beta", "og alpha")
)
tg <- as_tidygenomes(genes)
tg <- add_patterns(tg)
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