Classyfire R Manual

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Package ‘classyfireR’
August 31, 2018
Type Package
Title R Interface to the ClassyFire RESTful API
Version 0.1.0
Date 2018-06-13
Description Access to the ClassyFire RESTful API (http://classyfire.wishartlab.com).
Depends magrittr
Imports httr, jsonlite, tibble, crayon, clisymbols
Suggests testthat, covr, dplyr, purrr
License GPL (>= 3)
Encoding UTF-8
LazyData true
URL https://github.com/wilsontom/classyfireR
BugReports https://github.com/wilsontom/classyfireR/issues
RoxygenNote 6.1.0
Roxygen list(markdown = TRUE)
NeedsCompilation no
Author Tom Wilson [aut, cre]
Maintainer Tom Wilson 

R topics documented:
entity_classification .
get_status_code . . .
retrieve_classification
submit_classification

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1

2

entity_classification

entity_classification Entity Classification

Description
Retrive entity classification from ‘http://classyfire.wishartlab.com/entities/’
Usage
entity_classification(inchi_key)
Arguments
inchi_key

a character string of a valid InChIKey

Value
a tibble containing the following;
• Level Classification level (kingdom, superclass, class and subclass)
• Classification The compound classification
• CHEMONT Chemical Ontology Identification code
Examples
# Valid InChI key where all four classification levels are available
entity_classification('BRMWTNUJHUMWMS-LURJTMIESA-N')
# Valid InChI key where only three classification levels are available
entity_classification('MDHYEMXUFSJLGV-UHFFFAOYSA-N')
# Invalid InChI key
entity_classification('MDHYEMXUFSJLGV-UHFFFAOYSA-B')
# Using `dplyr` a vector of InChI Keys can be submitted and easily parsed
library(dplyr)
library(purrr)
keys <- c(
'BRMWTNUJHUMWMS-LURJTMIESA-N',
'XFNJVJPLKCPIBV-UHFFFAOYSA-N',
'TYEYBOSBBBHJIV-UHFFFAOYSA-N',
'AFENDNXGAFYKQO-UHFFFAOYSA-N',
'WHEUWNKSCXYKBU-QPWUGHHJSA-N',
'WHBMMWSBFZVSSR-GSVOUGTGSA-N')
classification_list <- map(keys, entity_classification)

get_status_code

get_status_code

3

Get Status Code

Description
Get Status Code
Usage
get_status_code(query_id)
Arguments
query_id

a numeric value for the query id

Value
a list of query_id and classification status; either In progress or Done
Examples
get_status_code(2813259)

retrieve_classification
Retrieve classification results

Description
Retrieve classification results from a new submission
Usage
retrieve_classification(query_id)
Arguments
query_id

a numeric value for the query id

Value
a tibble containing the following;
• Level Classification level (kingdom, superclass, class and subclass)
• Classification The compound classification
• CHEMONT Chemical Ontology Identification code

4

submit_classification

submit_classification Submit InChI Code for Classification

Description
Submit and new entity for classification using the ClassyFire webserver
Usage
submit_classification(query, label, type = "STRUCTURE")
Arguments
query

a charatcer string of InChI Code or SMILE

label

a character string of the query name

type

the label type (Default = STRUCTURE)

Value
if the classification has completed; a tibble containing the following;
• Level Classification level (kingdom, superclass, class and subclass)
• Classification The compound classification
• CHEMONT Chemical Ontology Identification code

Index
entity_classification, 2
get_status_code, 3
retrieve_classification, 3
submit_classification, 4

5



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