Package 'SNPannotator'

Run the annotation pipeline on a list of variants from shiny app

Description

This function should not be used outside shiny app A list of variants and parameters are received and their information is checked on various API servers.

Usage

annotate_shiny(config.list)

Arguments

config.list

List. A list of variants andconfiguration parameters.

Value

a data table with all variant information is returned.

---

Demo run of the annotation pipeline

Description

This function is a demo of the annotation algorithm.

Usage

demo_annotation()

Value

A data table containing the variant information for testing is returned. Report files are also saved in the current working directory.

---

List population from human database (1000 Genomes project)

Description

This function list the name, description and size of the available populations in 1000 Genomes project database. This database will be used for returning variables in high LD with the target SNP.

Usage

EnsemblDatabases(server = "https://rest.ensembl.org")

Arguments

server

Ensemble API end point. default: https://rest.ensembl.org

Value

A data table is returned which includes the name, description and size of the available populations in 1000 Genomes project database.

---

data release available on this REST server.

Description

Shows the data releases available on this REST server. May return more than one release (infrequent non-standard Ensembl configuration).

Usage

EnsemblReleases(server = "https://rest.ensembl.org")

Arguments

server

Ensemble API end point. default: https://rest.ensembl.org

Value

a message is displayed to the user

---

Query GTEx portal for Variant's genomic position based on rsID Retrieves variant information from the GTEx portal using either an rsID or a variant ID formatted as CHR_POS_REF_ALT. If an rsID is provided, the function returns the corresponding genomic positions in both GRCh37 and GRCh38 builds. When searching for an rsID based on genomic position, the position parameter should be specified according to the GRCh38 reference genome.

Description

Query GTEx portal for Variant's genomic position based on rsID Retrieves variant information from the GTEx portal using either an rsID or a variant ID formatted as CHR_POS_REF_ALT. If an rsID is provided, the function returns the corresponding genomic positions in both GRCh37 and GRCh38 builds. When searching for an rsID based on genomic position, the position parameter should be specified according to the GRCh38 reference genome.

Usage

findGenomicPos(id, type = "rsid", file_path = NULL)

Arguments

id	Character string representing the rsID (e.g., "rs12345") or the variant ID in the format "CHR_POS_REF_ALT" (e.g., "1_1234567_A_T"), depending on type.
type	Character string specifying the type of query. Must be either "rsid" or "varid".
file_path	character, path to a file for saving results as Excell spreadsheet.

Value

A data.table containing variant information including:

• rsid: variant id in rsID format

• chromosome: chromosome number

• position_b37: genomic position

• position_b38: genomic position

• ref: reference allele

• alt: alternate allele

---

Computes and returns LD values between the given variants.

Description

This function returns a data frame of LD values between the given variants in a selected population.

Usage

findPairwiseLD(
  rsList,
  file = NULL,
  pairwise = FALSE,
  build = 38,
  db = "1000GENOMES:phase_3:EUR",
  r2 = 0.1
)

Arguments

rsList	A vector of rs numbers.
file	Path to the Excel file for saving search results.
pairwise	If TRUE, compute pairwise LD between all elements of a list. If FALSE, computes the LD between first and other elements of the list. default: FALSE
build	Genome build. Either 37 or 38. default: 38
db	The population database for calculating LD scores. This can be found using Ensembl.Databases() function. default: "1000GENOMES:phase_3:EUR"
r2	Only return pairs of variants whose r-squared value is equal to or greater than the value provided. default: 0.1.

Value

A data table with variant information.

---

Finds variants in high LD

Description

This function returns a list of variables that are in high LD with a list of selected variants using data from the Ensembl website.

Usage

findProxy(
  rslist,
  file = NULL,
  build = "38",
  db = "1000GENOMES:phase_3:EUR",
  window_size = 500,
  r2 = 0.8
)

Arguments

rslist	A vector of rs numbers.
file	Path to the Excel file for saving search results.
build	Genome build. Either 37 or 38. default: 38
db	The population database for calculating LD scores. This can be found using Ensembl.Databases() function. default: 1000GENOMES:phase_3:EUR
window_size	Number of base pairs around the variant for checking LD scores (max = 500kb). default: 500
r2	The minimum LD threshold for selecting variants around the target SNP. default: 0.8.

Value

A data table with variant information.

---

Query Ensembl for variant information based on genomic position

Description

This function retrieves variant information from Ensembl based on the specified genomic position. It takes the chromosome number, start position, and end position as input parameters and searches for variants within this window, using the specified genomic build. If only the start position is provided, the function automatically sets the end position equal to the start position. This is particularly relevant for SNP variants, where the start and end positions are the same. The function returns all variants found within the defined window.

Usage

findRSID(
  chromosome,
  start_position,
  end_position = NULL,
  build = "38",
  file_path = NULL
)

Arguments

chromosome	Numeric, specifying the chromosome number.
start_position	Numeric, specifying the starting base pair position.
end_position	Numeric, specifying the ending base pair position.
build	Numeric, specifying the genomic build, default value is 38.
file_path	character, path to a file for saving results as Excell spreadsheet.

Value

A data.table containing variant information including:

• id: variant id in rsID format

• alleles: variant alleles

• seq_region_name: chromosome number

• start: starting base pair

• end: ending base pair

---

Find variant synonyms from Ensembl

Description

Retrieves synonym rsIDs for a set of variants using the Ensembl REST API. The input must be a character vector of variant identifiers in rsID format (e.g., "rs12345"). The function returns a data.table mapping each input rsID to any synonyms reported by Ensembl.

Usage

findSynonyms(rsids, build = "38", keepRSOnly = TRUE)

Arguments

rsids	A character vector of variant identifiers in rsID format.
build	Numeric. Genome build to query. Supported values are 37 and 38. Defaults to 38.
keepRSOnly	Logical. If TRUE, only synonyms starting with 'rs' will be retained in the output.

Value

A data.table with the following columns:

input_rsid

The input variant identifier.

updated_rsid

The updated variant identifier.

synonym

A synonym rsID reported by Ensembl.

---

Copy a sample configuration file

Description

This function provides a sample configuration file. The user can modify the parameters as desired

Usage

getConfigFile(dir.path)

Arguments

dir.path

The existing folder for copying the file.

---

Merge multiple inSilico annotation output objects and export to Excel

Description

This function loads multiple result objects produced by SNPannotator package. It merges the relevant tables (e.g., input variants, configuration, ...) across all objects and exports the combined results to a single Excel file. Optionally, it can trigger annotation and enrichment analyses using the STRING database.

Usage

merge_annotations(file_names, project_name, STRING = FALSE, ...)

Arguments

file_names	Character vector. Paths to the annotation output .rds files to merge. Each file should be a result object containing tables with variant, input, and configuration data.
project_name	Character. The project name used for naming the output Excel file and the log file.
STRING	Logical. If TRUE, performs annotation and enrichment analysis using STRING for the merged data.
...	Optional. Additional parameters passed to internal functions.

Value

Writes an object file, graphs and an Excel file with merged annotation results to disk as a side effect. The output file contains separate sheets for different data types.

Examples

## Not run: 
merge_annotations(
  file_names = c("output1.rds", "output2.rds", "output3.rds"),
  project_name = 'project1' )

## End(Not run)

---

Checks if the service is alive

Description

This function test whether the Ensembl server is accessible or not

Usage

pingEnsembl(server)

Arguments

server

name of the server. "https://rest.ensembl.org" can be used for GRCh38 and "https://grch37.rest.ensembl.org" for GRCh37.

Value

a message is displayed to the user

---

Run the annotation pipeline on a list of variants

Description

This function receives the path to the configuration file. A list of variants is received and their information is checked on various API servers.

Usage

run_annotation(configurationFilePath, verbose = TRUE)

Arguments

configurationFilePath	Character. The path to the configuration file.
verbose	Logical. Whether to display messages in the console.

Value

A data table containing all variant information is returned based on the user's selected specifications and parameters. Report files in various formats, including text, HTML, Excel, and image, are saved in the output folder.

---

Analyze STRING DB Interactions and perform functional enrichment

Description

This function takes a vector of gene symbols, retrieves their interaction partners from STRING DB, and performs functional enrichment analysis.

Usage

run_stringdb_annotation(name, gene_list, required_score = 700, limit = 0, ...)

Arguments

name	A character string specifying a unique identifier for this analysis run.
gene_list	A character vector of gene symbols (e.g., HGNC symbols or Ensembl gene IDs).
required_score	Threshold of significance to include an interaction, a number between 0 and 1000.
limit	Limits the number of interaction partners retrieved per protein, a number between 0 and 100.
...	Additional arguments passed to downstream functions for extended customization.

Value

set of report files, including images, text and excel files containing functional enrichment analysis results.

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