annotate {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)