get_common_ancestor: Generate the in_group

In trvinh/test: PhyloProfile

Description

Generate the in_group

Usage

get_common_ancestor(in_group, rank, name_list, selected_in_group, 
    ncbi_id_list)

Arguments

in_group	list of taxa
rank	selected rank
name_list	contains "ncbiID", "fullName", "rank", "parentID"
selected_in_group	contains "abbrName, "ncbiID", fullName", "strain", "genus"..
ncbi_id_list	list of input taxon IDs

Value

common anchestor

Author(s)

Carla Mölbert ([e-mail])

Examples

in_group <- c("Aeropyrum pernix", "Agrobacterium fabrum")
rank <- "species"
name_list_file <- system.file(
    "extdata", "data/taxonNamesFull.txt",
    package = "phyloprofile", mustWork = TRUE
)
name_list <- as.data.frame(data.table::fread(name_list_file))
selected_in_group <- get_taxonomy_matrix(FALSE, NULL)
ncbi_id_list <- c(56636, 1176649)
get_common_ancestor(
    in_group,
    rank,
    name_list,
    selected_in_group,
    ncbi_id_list
)

trvinh/test documentation built on May 9, 2019, 2:26 a.m.