Package 'queryup'

Accessory function used to build the query url

Description

Accessory function used to build the query url

Usage

build_query_url(
  query = NULL,
  base_url = "https://rest.uniprot.org/uniprotkb/",
  columns = c("accession", "id", "gene_names", "organism_name", "reviewed"),
  format = "json"
)

Arguments

query	list of keys corresponding to UniProt's query fields. For example : list("gene_exact" = c("Pik3r1", "Pik3r2") , "organism" = c("10090", "9606"), "reviewed" = "yes")
base_url	The base url for the UniProt REST API
columns	names of UniProt data columns to retrieve.
format	format of the response provided by the UniProt API

Value

the query url

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Accessory function removing invalid values from a query

Description

Accessory function removing invalid values from a query

Usage

clean_query(query, df)

Arguments

query	list of keys corresponding to UniProt's query fields. For example : list("gene_exact" = c("Pik3r1", "Pik3r2") , "organism" = c("10090", "9606"), "reviewed" = "yes")
df	data.frame with invalid values (in column "value") and corresponding query field (in column "field").

Value

the input query without the invalid values

---

Retrieve data from UniProt using UniProt's REST API

Description

Retrieve data from UniProt using UniProt's REST API

Usage

get_uniprot_data(
  query = NULL,
  base_url = "https://rest.uniprot.org/uniprotkb/",
  columns = c("accession", "id", "gene_names", "organism_id", "reviewed")
)

Arguments

query	list of keys corresponding to UniProt's query fields. For example : list("gene_exact" = c("Pik3r1", "Pik3r2") , "organism" = c("10090", "9606"), "reviewed" = "yes"). See 'query_fields' for available query fields.
base_url	The base url for the UniProt REST API
columns	names of UniProt data columns to retrieve. Examples include "accession", "id", "gene_names", "keyword", "sequence". See 'return_fields' for available return fields.

Value

a list with the following items :

url

the query url

status

the http status code for the request

messages

messages returned by the REST API

content

a data.frame containing the query results

Examples

#Getting gene names, keywords and protein sequences for a set of UniProt IDs.
ids <- c("P22682", "P47941")
cols <- c("accession", "id", "gene_names", "keyword", "sequence")
query = list("accession_id" = ids)
df <- get_uniprot_data(query = query, columns = cols)$content
df

---

Accessory function retrieving invalid values from messages returned by the UniProt API.

Description

Accessory function retrieving invalid values from messages returned by the UniProt API.

Usage

parse_messages(messages)

Arguments

messages

character string containing the error messages returned by UniProt API

Value

a data.frame with invalid values (in column "value") and corresponding query field (in column "field"). NULL if no invalid values are identified.

---

Available query fields.

Description

Query fields that can be used to generate queries using 'queryup' along with associated examples and description.

Usage

query_fields

Format

A data frame with 44 rows and 3 variables:

field

Name of the query field

example

Example query (as appearing in the query url)

description

Description of the example query

Source

https://www.uniprot.org/help/query-fields

---

Retrieve data from UniProt using UniProt's REST API.

Description

Retrieve data from UniProt using UniProt's REST API. To avoid non-responsive queries, they are split into smaller queries with at most max_keys items per query field. Not that it works only with queries where items within query fields are collapsed with '+OR+' and different query fields are collapsed with '+AND+' (see query_uniprot())

Usage

query_uniprot(
  query = NULL,
  base_url = "https://rest.uniprot.org/uniprotkb/",
  columns = c("accession", "id", "gene_names", "organism_id", "reviewed"),
  max_keys = 200,
  updateProgress = NULL,
  show_progress = TRUE
)

Arguments

query	list of keys corresponding to UniProt's query fields. For example : query = list("gene_exact" = c("Pik3r1", "Pik3r2"), "organism_id" = c("10090", "9606"), "reviewed" = "true"). See 'query_fields' for available query fields.
base_url	The base url for the UniProt REST API
columns	names of UniProt data columns to retrieve. Examples include "accession", "id", "genes", "keywords", "sequence". See 'return_fields' for available return fields.
max_keys	maximum number of field items submitted
updateProgress	used to display progress in shiny apps
show_progress	Show progress bar

Value

a data.frame

Examples

# Get the UniProt entries of all proteins encoded by gene Pik3r1
ids <- c("P22682", "P47941")
query = list("accession_id" = ids)
df <-  query_uniprot(query = query)
head(df)

---

Available return fields ("columns").

Description

Return fields that can be retrieved using 'queryup' along with their label (column "Label") as appearing in the retrieved data.frame.

Usage

return_fields

Format

A data frame with 287 rows and 2 variables:

field

Name of the returned field

label

Label of the corresponding column in the retrieved data.frame

Source

https://www.uniprot.org/help/return_fields

---

Information for 1000 UniProt entries from the organism Mus musculus

Description

Entry names and other attributes of 1000 UniProt entries in Mus musculus.

Usage

uniprot_entries

Format

A data frame with 1000 rows and 5 variables:

Entry

UniProt entry accession id

Entry Name

UniProt entry name

Gene Names

Gene names

Organism (ID)

Taxon ID

Reviewed

Swiss-Prot review status

Source

https://www.uniprot.org/

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