classyfireR (version 0.2.2)

get_classification: Get Entity Classification

Description

Retrieve entity classification from `http://classyfire.wishartlab.com/entities/'

Usage

get_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

# NOT RUN {
# Valid InChI key where all four classification levels are available
get_classification('BRMWTNUJHUMWMS-LURJTMIESA-N')

# Valid InChI key where only three classification levels are available
get_classification('MDHYEMXUFSJLGV-UHFFFAOYSA-N')

# Invalid InChI key
get_classification('MDHYEMXUFSJLGV-UHFFFAOYSA-B')


# Using `dplyr` a vector of InChI Keys can be submitted and easily parsed
  library(dplyr)
  library(purrr)
  library(tidyr)

 keys <- c(
'BRMWTNUJHUMWMS-LURJTMIESA-N',
'XFNJVJPLKCPIBV-UHFFFAOYSA-N',
'TYEYBOSBBBHJIV-UHFFFAOYSA-N',
'AFENDNXGAFYKQO-UHFFFAOYSA-N')

 classification_list <- map(keys, get_classification)

 classification_list <- map(classification_list, ~{select(.,-CHEMONT)})

 spread_tibble <- purrr:::map(classification_list, ~{
                  spread(., Level, Classification)
                  }) %>% bind_rows() %>% data.frame()

 rownames(spread_tibble) <- keys

 classification_tibble <-  tibble(
     InChIKey = rownames(spread_tibble),
     Kingdom = spread_tibble$kingdom,
     SuperClass = spread_tibble$superclass,
     Class = spread_tibble$class,
     SubClass = spread_tibble$subclass,
     Level5 = spread_tibble$level.5,
     Level6 = spread_tibble$level.6,
     Level7 = spread_tibble$level.7
    )

 print(classification_tibble)
# }
# NOT RUN {

# }