Title:	Processing and Analysis of 'O-GlcNAcAtlas' Data
Version:	0.1.5
Description:	Provides tools for processing and analyzing data from the 'O-GlcNAcAtlas' database https://oglcnac.org/, as described in Ma (2021) <doi:10.1093/glycob/cwab003>. It integrates 'UniProt' https://www.uniprot.org/ API calls to retrieve additional information. It is specifically designed for research workflows involving 'O-GlcNAcAtlas' data, providing a flexible and user-friendly interface for customizing and downloading processed results. Interactive elements allow users to easily adjust parameters and handle various biological datasets.
License:	GPL-3
Encoding:	UTF-8
RoxygenNote:	7.3.2
Imports:	cli, httr, jsonlite, shiny, DT, bslib, readxl, glue
Suggests:	testthat (≥ 3.0.0), tibble, curl
Config/testthat/edition:	3
NeedsCompilation:	no
Packaged:	2025-02-19 06:16:16 UTC; Bach
Author:	Yaoxiang Li [aut, cre]
Maintainer:	Yaoxiang Li <liyaoxiang@outlook.com>
Repository:	CRAN
Date/Publication:	2025-02-19 09:30:02 UTC

Compare Input and Updated Tibbles

Description

This function compares the original input tibble and the updated tibble, identifying and reporting any changes in the specified columns ('entry_name', 'protein_name', 'gene_name').

Usage

compare_tibbles_uniprot(
  original_tibble,
  updated_tibble,
  entry_name_col = "entry_name",
  protein_name_col = "protein_name",
  gene_name_col = "gene_name"
)

Arguments

Value

None. Prints the differences between the tibbles.

Examples

# Example usage:

# Original input tibble
input_data <- tibble::tibble(
  id = c(1, 2),
  species = c("mouse", "rat"),
  sample_type = c("brain", "liver"),
  accession = c("O88737", "Q9R064"),
  accession_source = c("UniProt", "UniProt")
)

# Process the tibble (this will add the entry_name, protein_name, and gene_name)
processed_data <- process_tibble_uniprot(input_data)

# Compare the original and processed tibbles
compare_tibbles_uniprot(input_data, processed_data)

Launch oglcnac Shiny App

Description

This function launches a Shiny App for uploading, processing, and downloading UniProt data in CSV, TSV, or Excel format. Users can upload data, preview it, and select specific columns for processing. The processed data can be viewed and downloaded.

Usage

launch_app()

Value

None

Examples

if (interactive()) {
  oglcnac::launch_app()
}

Parse UniProt Data

Description

This function parses the data retrieved from the UniProt API to extract the entry name, protein name, and gene name.

Usage

parse_uniprot_data(uniprot_data)

Arguments

Value

A list containing 'entry_name', 'protein_name', and 'gene_name'.

Examples

# Example usage:

# Retrieve UniProt data
test_result <- retrieve_uniprot_data("O88737")

# Parse the UniProt data
parsed_result <- parse_uniprot_data(test_result)

# Print the parsed result
print(parsed_result)

Process a Tibble of UniProt Data

Description

This function processes a tibble containing accession and accession_source columns. It retrieves data from the UniProt API for rows with accession_source == "UniProt" and overwrites or creates the entry_name, protein_name, and gene_name columns only if the parsed values are not NULL or NA.

Usage

process_tibble_uniprot(
  data,
  accession_col = "accession",
  accession_source_col = "accession_source",
  entry_name_col = "entry_name",
  protein_name_col = "protein_name",
  gene_name_col = "gene_name"
)

Arguments

Value

A tibble with UniProt data processed.

Examples

# Example usage:

# Load necessary library
library(tibble)

# Reduced example data as an R tibble
test_data <- tibble::tibble(
  id = c(1, 78, 83, 87),
  species = c("mouse", "mouse", "rat", "mouse"),
  sample_type = c("brain", "brain", "brain", "brain"),
  accession = c("O88737", "O35927", "Q9R064", "P51611"),
  accession_source = c("OtherDB", "UniProt", "UniProt", "UniProt"),
  entry_name = c("BSN_MOUSE", NA, "GORS2_RAT", NA),
  protein_name = c("Protein bassoon", NA, "Golgi reassembly-stacking protein2", NA),
  gene_name = c("Bsn", NA, "Gorasp2", NA)
)

# Process the tibble
result_data <- process_tibble_uniprot(test_data)

# Compare the original and processed tibbles
compare_tibbles_uniprot(test_data, result_data)

Retrieve Data from UniProt API

Description

This function sends a GET request to the UniProt REST API and retrieves data based on the provided UniProt accession number.

Usage

retrieve_uniprot_data(accession)

Arguments

Value

A list containing the retrieved data in JSON format, or NULL if the request fails.

Examples

# Example usage

result <- retrieve_uniprot_data("O88737")
print(result)