Classyfire R Manual
User 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 <tpw2@aber.ac.uk>
Rtopics documented:
entity_classification..................................... 2
get_status_code....................................... 3
retrieve_classification.................................... 3
submit_classification .................................... 4
Index 5
1
2entity_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
atibble 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 3
get_status_code 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
atibble containing the following;
•Level Classification level (kingdom, superclass, class and subclass)
•Classification The compound classification
•CHEMONT Chemical Ontology Identification code
4submit_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
