JunctionType: Annotates the junctions in a bed file.

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

Description

For identified splice junctions from RNA-Seq, this function finds the junction types for each entry according to the given annotation. Six types of junctions are classified. find more details in the tutorial.

Usage

  JunctionType(jun, splicemax, txdb, ids, ...)

Arguments

jun	a GRange object for junctions, the output of function Bed2Range.
splicemax	a known exon splice matrix from the annotation.
txdb	a TxDb object.
ids	a dataframe containing gene/transcript/protein id mapping information.
...	additional arguments

Details

Go to https://genome.ucsc.edu/FAQ/FAQformat.html#format1 for more information about BED format.

Value

a data frame of type and source for each junction.

Author(s)

Xiaojing Wang

Examples

bedfile <- system.file("extdata/beds", "junctions1.bed", package="customProDB")
jun <-  Bed2Range(bedfile,skip=1,covfilter=5)
load(system.file("extdata/refseq", "splicemax.RData", package="customProDB"))
load(system.file("extdata/refseq", "ids.RData", package="customProDB"))
txdb <- loadDb(system.file("extdata/refseq", "txdb.sqlite",
            package="customProDB"))
junction_type <- JunctionType(jun, splicemax, txdb, ids)
table(junction_type[, 'jun_type'])

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