Annotates the junctions in a bed file.

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

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'])

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(customProDB)
Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: biomaRt
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/customProDB/JunctionType.Rd_%03d_medium.png", width=480, height=480)
> ### Name: JunctionType
> ### Title: Annotates the junctions in a bed file.
> ### Aliases: JunctionType
> 
> ### ** 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"))
Loading required package: GenomicFeatures
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
> junction_type <- JunctionType(jun, splicemax, txdb, ids)
> table(junction_type[, 'jun_type'])

connect a known exon and a region overlap with known exon 
                                                        1 
                              connect two non-exon region 
                                                        9 
                                           known junction 
                                                       46 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>