Package 'SNPannotator'

Run the annotation pipeline on a list of variants

Description

This function receives a list of variants and checks their information on Ensembl website via the Ensembl REST API server.

Usage

annotate(
  rslist,
  server,
  db,
  outputPath,
  window_size = 500,
  r2 = 0.5,
  LDlist = TRUE,
  cadd = FALSE,
  geneNames.file = NULL,
  regulatoryType.file = NULL,
  cores = 0
)

Arguments

rslist	A vector of rs numbers.
server	Name of the server. "https://rest.ensembl.org" can be used for GRCh38 and "https://grch37.rest.ensembl.org" for GRCh37.
db	The population database for calculating LD scores. This can be found using listDatabases function.
outputPath	The report file will be saved in this path as an Excel file (.xlsx)
window_size	Number of base pairs around the variant for checking LD scores (max = 500kb)
r2	The LD threshold for selecting variants around the target SNP.
LDlist	If set to TRUE, variants in high LD will be found and added to the output.
cadd	If set to TRUE, the CADD scores will be added to variant information.
geneNames.file	path the gene information file (*.rds). Default value is NULL and ENSEMBL website will be checked if no file is provided.
regulatoryType.file	path the variants regulatory type information file (*.rds). Default value is NULL and this step will be skipped if no file is provided.
cores	set to a value above 0 for parallel processing.

Value

a data table with all variant information is returned.

Examples

## Not run: 
# select the required server
server <- "https://grch37.rest.ensembl.org"

# select the database for population data
# this can be selected from listDatabases() function
db <- "1000GENOMES:phase_3:EUR"

# create a vector of required SNPs
rslist=c('rs236349')

output <- annotate(rslist,server,db,
  outputPath = paste(tempdir(),'sampleOutput.xlsx',sep="/"),
  window_size = 500,
  r2 = .9,
  cadd = FALSE)
  
## End(Not run)

---

Find variants in high LD with the lead SNP.

Description

This function returns a list of variables that are in high LD with the lead variant.

Usage

LDlist(rslist, server, db, window_size, r2)

Arguments

rslist	A vector of rs numbers.
server	Name of the server. "https://rest.ensembl.org" can be used for GRCh38 and "https://grch37.rest.ensembl.org" for GRCh37.
db	The population database for calculating LD scores. This can be found using listDatabases function.
window_size	Number of base pairs around the variant for checking LD scores (max = 500kb)
r2	The LD threshold for selecting variants around the target SNP.

Value

a data table with variant information.

---

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

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

---

Checks if the service is alive

Description

This function test whether the Ensembl server is accessible or not

Usage

pingServer(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

---

Shows the data releases available on this REST server.

Description

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

Usage

releaseVersion(server)

Arguments

server

name of the server.

Value

a message is displayed to the user

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