JunctionType: Annotates the junctions in a bed file.

Description Usage Arguments Details Value Author(s) Examples

View source: R/JunctionType.R

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

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  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

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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.