Help for package SNPannotator

Type:

Package

Title:

Investigating the Functional Characteristics of Selected Variants and Their Vicinity Genomic Region

Version:

1.4.0

Date:

2025-11-15

Author:

Alireza Ani [aut, cre], Zoha Kamali [aut], Ahmad Vaez [aut]

Maintainer:

Alireza Ani <a.ani@umcg.nl>

Depends:

R (≥ 4.0)

Imports:

data.table (≥ 1.15.4), httr (≥ 1.4.7), jsonlite (≥ 1.8.8), xml2 (≥ 1.3.6), openxlsx (≥ 4.2.5.2), progress (≥ 1.2.3), ggplot2 (≥ 3.5.1), kableExtra (≥ 1.4.0), methods (≥ 4.2.0), rmarkdown (≥ 2.26), ini (≥ 0.3.1), igraph (≥ 2.0.3), ggraph (≥ 2.2.1), futile.logger (≥ 1.4.3), png , readr (≥ 2.1.5)

Description:

To investigate the functional characteristics of selected SNPs and their vicinity genomic region. Linked SNPs in moderate to high linkage disequilibrium (e.g. r2>0.50) with the corresponding index SNPs will be selected for further analysis.

URL:

https://cran.r-project.org/package=SNPannotator

License:

GPL-3

Encoding:

UTF-8

RoxygenNote:

7.3.2

Suggests:

knitr

VignetteBuilder:

knitr

NeedsCompilation:

Packaged:

2025-11-15 19:49:27 UTC; Alireza

Repository:

CRAN

Date/Publication:

2025-11-16 10:10:02 UTC

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(build = 38)

Arguments

build

Genome build. Either 37 or 38. default: 38

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(build = 38)

Arguments

build

Genome build. Either 37 or 38. default: 38

Value

a message is displayed to the user

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.

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

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 output files

Description

This function merges multiple result files into one.

Usage

mergeResultFiles(..., fileName)

Arguments

...

list of input files to be merged.

fileName

name of the output file.

Value

A data table is returned.

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.