customProDB (version 1.12.0)

Varlocation: Annotates the variations with genomic location.

Description

For a given GRange object of variations, the Varlocation() function finds the genomic locations for each entry according to the given annotation. Seven labels are used to describe the location (intergenic, intro_nonProcoding, exon_nonProcoding, intron, 5utr, 3utr and coding). details of the definition can be found in the tutorial.

Usage

Varlocation(Vars, txdb, ids, ...)

Arguments

Vars

a GRange object of variations

txdb

a TxDb object.

ids

a dataframe containing gene/transcript/protein id mapping information

...

additional arguments

Value

a data frame of locations for each variation

Details

see 'introduction' for more details

Examples

## Not run: 
# vcffile <- system.file("extdata/vcfs", "test1.vcf", package="customProDB")
# vcf <- InputVcf(vcffile)
# 
# table(values(vcf[[1]])[['INDEL']])
# index <- which(values(vcf[[1]])[['INDEL']] == TRUE)
# indelvcf <- vcf[[1]][index]
# 
# index <- which(values(vcf[[1]])[['INDEL']] == FALSE)
# SNVvcf <- vcf[[1]][index]
# 
# txdb <- loadDb(system.file("extdata/refseq", "txdb.sqlite", package="customProDB"))
# load(system.file("extdata/refseq", "ids.RData", package="customProDB"))
# SNVloc <- Varlocation(SNVvcf,txdb,ids)
# indelloc <- Varlocation(indelvcf,txdb,ids)
# table(SNVloc[,'location'])
# ## End(Not run)