Varlocation: Annotates the variations with genomic location.

In customProDB: Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search

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

Details

see 'introduction' for more details

Value

a data frame of locations for each variation

Author(s)

Xiaojing Wang

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)

customProDB documentation built on Nov. 8, 2020, 8:06 p.m.