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Last data update: 2014.03.03

R: Generate a GRanges objects from BED file.

Bed2Range

R Documentation

Generate a GRanges objects from BED file.

Description

Read BED file into a GRanges object. This function requires complete BED file. Go to https://genome.ucsc.edu/FAQ/FAQformat.html#format1 for more information about BED format.

Usage

  Bed2Range(bedfile, skip = 1, covfilter = 5, ...)

Arguments

`bedfile`	a character contains the path and name of a BED file.
`skip`	the number of lines of the BED file to skip before beginning to read data, default 1.
`covfilter`	the number of minimum coverage for the candidate junction, default 5.
`...`	additional arguments

Details

Read BED file contain junctions into a GRanges object.

Value

a GRanges object containing all candidate junctions from the BED file.

Author(s)

Xiaojing Wang

Examples

bedfile <- system.file("extdata/beds", "junctions1.bed", package="customProDB")
jun <-  Bed2Range(bedfile, skip=1,covfilter=5)
length(jun)

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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Type 'demo()' for some demos, 'help()' for on-line help, or
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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/Bed2Range.Rd_%03d_medium.png", width=480, height=480)
> ### Name: Bed2Range
> ### Title: Generate a GRanges objects from BED file.
> ### Aliases: Bed2Range
> 
> ### ** Examples
> 
> bedfile <- system.file("extdata/beds", "junctions1.bed", package="customProDB")
> jun <-  Bed2Range(bedfile, skip=1,covfilter=5)
> length(jun)
[1] 56
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>