Package 'protean'

Title: Sequence Profiles of OncoKB Genes
Description: A data package of sequence profiles of OncoKB genes. These profiles are obtained via Ensembl's REST API and derived from the pairwise alignment of the human sequence with its orthologs.
Authors: Ramiro Magno [aut, cre] (ORCID: <https://orcid.org/0000-0001-5226-3441>), Isabel Duarte [aut] (ORCID: <https://orcid.org/0000-0003-0060-2936>), Ana-Teresa Maia [aut] (ORCID: <https://orcid.org/0000-0002-0454-9207>), CINTESIS [cph, fnd]
Maintainer: Ramiro Magno <[email protected]>
License: CC BY 4.0
Version: 0.1.2
Built: 2026-05-22 05:58:27 UTC
Source: https://github.com/maialab/protean

Help Index

Download OncoKB Cancer Gene List

Description

Download OncoKB Cancer Gene List

Usage

download_gene_list(
  path = stop("`path` must be specified"),
  url = oncokb_dwl_url()
)

Arguments

path

A character string with the file path where the downloaded file is to be saved. Tilde-expansion is performed.
url

The URL of the resource providing the OncoKB cancer gene list.

Exported genes

Description

A character vector of genes for which the retrieval of sequence profiles was successful and are hence provided with this package.

Usage

exported_genes

Format

A character vector.

Fetch current OncoKB genes

Description

fetch_oncokb_genes() retrieves the current set of OncoKB genes from an OncoKB's cancer gene list file.

Usage

fetch_oncokb_genes(file = oncokb_dwl_url())

Arguments

file

A URL or a file path to the source providing the cancer gene list file. By default it will automatically download cancerGeneList.tsv from OncoKB website.

Value

A character vector of gene names.

Examples

fetch_oncokb_genes()

Get sequence profiles

Description

This function retrieves pairwise alignments between the human sequence queried in symbol and each of its orthologs via Ensembl's REST API ⁠homology/symbol/:species/:symbol⁠ endpoint. Then, from these alignments, sequence profiles are derived.

Usage

get_profile(symbol, simplify = TRUE)

Arguments

symbol

A character vector of HUGO gene symbols.
simplify

Should the result be simplified if only one gene symbol is queried. If TRUE, then in the case only one gene symbol is queried the result is not a list of one tibble, but the tibble itself.

Value

A list of tibbles, one for each gene symbol queried, with the following columns:

timestamp

Date and time of the download from Ensembl.

human_prot_id

Ensembl identifier of the human protein sequence.

ortho_prot_id

Ensembl identifier of the ortholog protein sequence.

ortho_species

Species name of the ortholog sequence.

human_align_seq

In the context of pairwise alignment between the human sequence and one of its orthologs, this is the aligned human sequence.

ortho_align_seq

In the context of pairwise alignment between the human sequence and one of its orthologs, this is the aligned ortholog sequence.

human_ortho_perc_id

Percentage of the human sequence matching the sequence of the ortholog.

ortho_human_perc_id

Percentage of the orthologous sequence matching the human sequence.

human_profile_id

Human protein sequence.

ortho_profile_seq

Orthologous sequence stripped off of the alignment positions which correspond to gaps in the human sequence.

Missing genes

Description

A character vector of genes for which the retrieval of sequence profiles was not successful and are therefore absent.

Usage

missing_genes

Format

A character vector.

OncoKB genes

Description

A character vector of OncoKB genes used as query to retrieve the sequence profiles bundled with this package.

Usage

oncokb_genes

Format

A character vector.

Get the path to a sequence profile

Description

protean comes bundled with a number of sequence profile files in its inst/profiles directory. This function make them easy to access by returning the local path to them.

Usage

profile_path(file = NULL)

Arguments

file

Name of file or gene symbol. If NULL, the profile files will be listed.

Examples

# Retrieve the path to the sequence profile of the TP53 protein
# Using the gene symbol
profile_path("TP53")

# Using the file name
profile_path("TP53.csv.gz")

# List all profile files
profile_path()

Read a sequence profile

Description

Read a sequence profile

Usage

read_profile(file = stop("`file` must be specified"), sort = TRUE)

Arguments

file

A path to a sequence profile file.
sort

Whether to sort the sequences by the variable human_ortho_perc_id, from highest (most similar to human) to lowest (most distant from human).

Value

A tibble of 10 variables:

timestamp

Date and time of the download from Ensembl.

human_prot_id

Ensembl identifier of the human protein sequence.

ortho_prot_id

Ensembl identifier of the ortholog protein sequence.

ortho_species

Species name of the ortholog sequence.

human_align_seq

In the context of pairwise alignment between the human sequence and one of its orthologs, this is the aligned human sequence.

ortho_align_seq

In the context of pairwise alignment between the human sequence and one of its orthologs, this is the aligned ortholog sequence.

human_ortho_perc_id

Percentage of the human sequence matching the sequence of the ortholog.

ortho_human_perc_id

Percentage of the orthologous sequence matching the human sequence.

human_profile_id

Human protein sequence.

ortho_profile_seq

Orthologous sequence stripped off of the alignment positions which correspond to gaps in the human sequence.

Examples

read_profile(profile_path("TP53"))