initUTRAnnotation: Query transcripts regions and sequences from Ensembl database

In utr.annotation: Annotate Variants in the Untranslated Regions

Description

initUTRAnnotation query transcripts regions, UTRs and coding sequences from Ensembl database, which will be used by runUTRAnnotation to do UTR annotation.

Usage

initUTRAnnotation(
  variantFile,
  species,
  ensemblVersion,
  getTranscript = TRUE,
  format = "csv",
  dataDir = NULL,
  verbose = FALSE
)

Arguments

variantFile	a CSV file with Chr, Pos, Ref, Alt
species	either human or mouse
ensemblVersion	(optional) a number specifying which version of Ensembl annotation you'd like to use, by default use the latest version
getTranscript	(optional) Whether to get ids of the transcripts that overlap with all the variants. If the number of variants is too large (for example > 100,000), set it to FALSE and do this in runUTRAnnotation on each partition in parallel.
format	(optional) csv or vcf, the default is csv
dataDir	(optional) path to the store the database information, if not specified will create a folder named as input variant file name with a "db_" prefix
verbose	Whether print diagnostic messages. The default is FALSE.

Value

A variant table with Transcript column which contains the ids of the transcripts that overlap with the variants

Examples

test_variant_file <- system.file("extdata", "variants_sample.csv", package = "utr.annotation")
initUTRAnnotation(variantFile = test_variant_file,
                  species = "human",
                  ensemblVersion = 93,
                  dataDir = "test_db")

utr.annotation documentation built on Aug. 23, 2021, 9:06 a.m.