| Type: | Package |
| Title: | Investigating the Functional Characteristics of Selected SNPs and Their Vicinity Genomic Region |
| Version: | 0.2.6.0 |
| Date: | 2023-01-12 |
| Author: | Alireza Ani [aut, cre], Zoha Kamali [aut], Ahmad Vaez [aut] |
| Maintainer: | Alireza Ani <a.ani@umcg.nl> |
| Depends: | R (≥ 3.5) |
| Imports: | data.table, httr, jsonlite, xml2, openxlsx, progress, doParallel, foreach, ggplot2, kableExtra, methods, rmarkdown |
| 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. |
| License: | GPL-3 |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.2.2 |
| NeedsCompilation: | no |
| Packaged: | 2023-01-12 09:33:50 UTC; Alireza |
| Repository: | CRAN |
| Date/Publication: | 2023-01-12 15:40:02 UTC |
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 |
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.
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 |
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)
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