Last data update: 2014.03.03

R: Bedgraph to TranscriptDb object
BED2txDbR Documentation

Bedgraph to TranscriptDb object

Description

Function to transform BED format file to Bioconductor TranscriptDb object

Usage

BED2txDb(input_bed_path)

Arguments

input_bed_path

Path to BED file. If 12 column BED provided, function is splice aware. If 6 column BED provided, function assumes no splicing.

Value

TranscriptDb object

Author(s)

Lukasz Jan Kielpinski, Nikos Sidiropoulos

Examples

write(strwrap("chr1\t134212702\t134229870\tENSMUST00000072177\t0\t+
             \t134212806\t134228958\t0\t8\t347,121,24,152,66,120,133,1973,
             \t0,8827,10080,11571,12005,13832,14433,15195,", width = 300),
      file="dummy.bed")
BED2txDb("dummy.bed")

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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'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(RNAprobR)
Loading required package: GenomicFeatures
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: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
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: plyr

Attaching package: 'plyr'

The following object is masked from 'package:IRanges':

    desc

The following object is masked from 'package:S4Vectors':

    rename

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/RNAprobR/BED2txDb.Rd_%03d_medium.png", width=480, height=480)
> ### Name: BED2txDb
> ### Title: Bedgraph to TranscriptDb object
> ### Aliases: BED2txDb
> 
> ### ** Examples
> 
> write(strwrap("chr1\t134212702\t134229870\tENSMUST00000072177\t0\t+
+              \t134212806\t134228958\t0\t8\t347,121,24,152,66,120,133,1973,
+              \t0,8827,10080,11571,12005,13832,14433,15195,", width = 300),
+       file="dummy.bed")
> BED2txDb("dummy.bed")
TxDb object:
# Db type: TxDb
# Supporting package: GenomicFeatures
# transcript_nrow: 1
# exon_nrow: 8
# cds_nrow: 0
# Db created by: GenomicFeatures package from Bioconductor
# Creation time: 2016-07-06 03:31:23 +0900 (Wed, 06 Jul 2016)
# GenomicFeatures version at creation time: 1.24.3
# RSQLite version at creation time: 1.0.0
# DBSCHEMAVERSION: 1.1
Warning message:
Using togroup() on a CompressedIRangesList object is deprecated. Please
  use togroup(PartitioningByWidth(...)) instead. 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>