R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> 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
>