Nothing
## ---- echo = FALSE, message = FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
options(width = 750)
knitr::opts_chunk$set(
comment = "#>",
error = FALSE,
tidy = FALSE)
## ---- eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # retrieving the taxonomic hierarchy of "Arabidopsis thaliana"
# # from NCBI Taxonomy
# myTAI::taxonomy( organism = "Arabidopsis thaliana",
# db = "ncbi",
# output = "classification" )
## ---- eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # retrieving the taxonomic hierarchy of "Arabidopsis thaliana"
# # from the Integrated Taxonomic Information System
# myTAI::taxonomy( organism = "Arabidopsis thaliana",
# db = "itis",
# output = "classification" )
## ---- eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # retrieving the taxonomy id of the query organism from NCBI Taxonomy
# myTAI::taxonomy( organism = "Arabidopsis thaliana",
# db = "ncbi",
# output = "taxid" )
## ---- eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # retrieving the taxonomy id of the query organism from Integrated Taxonomic Information Service
# myTAI::taxonomy( organism = "Arabidopsis",
# db = "itis",
# output = "taxid" )
## ---- eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # retrieve children taxa of the query organism stored in the correspondning database
# myTAI::taxonomy( organism = "Arabidopsis",
# db = "ncbi",
# output = "children" )
## ---- eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # retrieve children taxa of the query organism stored in the correspondning database
# myTAI::taxonomy( organism = "Arabidopsis",
# db = "itis",
# output = "children" )
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