partitionVariantFile: Partition the variant file to run in parallel

In utr.annotation: Annotate Variants in the Untranslated Regions

Description

partitionVariantFile is used to partition the variant file into small partition files by user defined size or number

Usage

partitionVariantFile(
  variantFile,
  chunkSize = NULL,
  chunkNum = NULL,
  chunkPath = "chunks",
  species,
  ensemblVersion = NULL,
  overwrite = FALSE,
  dataDir = NULL,
  getTranscript = TRUE,
  format = "csv",
  verbose = FALSE
)

Arguments

variantFile	variant file in CSV format
chunkSize	Partition the variant file into chunk files, which has a certain number of rows
chunkNum	Partition the variant file into a certain number of chunk files
chunkPath	(optional) A file directory to store all partition files. By default will output to "chunks" folder
species	human or mouse
ensemblVersion	(optional) a number specifying which version of Ensembl annotation you'd like to use, by default use the latest version
overwrite	(optional) If chunkPath already exists and not empty, whether or not to overwrite it. By default, do not overwrite and will raise error.
dataDir	(optional) path to store database information, if not specified will create a folder named as input variant file name with a "db_" prefix
getTranscript	(optional) Whether to get ids of the transcripts that overlap with all the variants. The default value is TRUE. 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
verbose	Whether print diagnostic messages. The default is FALSE.

Value

a list of partition variant files

Examples

variants_sample <- system.file("extdata", "variants_sample.csv", package = "utr.annotation")

# Partition variants_sample file equally into 3 variant files
# and store them in user specified chunkPath folder
partitionVariantFile(variantFile = variants_sample,
                     chunkNum = 3,
                     chunkPath = "chunks_3",
                     species = "human",
                     ensemblVersion = 93,
                     dataDir = "db_all_variants")

# Partition variants_sample file into smaller variant files each of which contains 7 variants,
# and store them in user specified chunkPath folder
partitionVariantFile(variantFile = variants_sample,
                     chunkSize = 7,
                     chunkPath = "chunks_7_vars",
                     species = "human",
                     ensemblVersion = 93,
                     dataDir = "db_all_variants")
unlink("db_all_variants", recursive = TRUE)
unlink("chunks_3", recursive = TRUE)
unlink("chunks_7_vars", recursive = TRUE)

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