Exporting data in norm_df data frame (product of dtcr, slograt and swinsor) to bedgraph format compatible with UCSC Genome Browser

Description

Function converts annotation from transcript to genomic coordinates and creates two-track bedgraph file (one track for each strand)

Usage

norm2bedgraph(norm_GR, txDb, bed_file, norm_method, genome_build,
  bedgraph_out_file = "out_file", track_name = "Track_name",
  track_description = "Track_description")

Arguments

Value

Function writes bedgraph file.

Author(s)

Lukasz Jan Kielpinski, Nikos Sidiropoulos

See Also

bedgraph2norm, norm_df2GR, dtcr, slograt, swinsor, compdata

Examples

dummy_euc_GR_control <- GRanges(seqnames="DummyRNA",
                                 IRanges(start=round(runif(100)*100),
                                 width=round(runif(100)*100+1)), strand="+",
                                 EUC=round(runif(100)*100))
dummy_euc_GR_treated <- GRanges(seqnames="DummyRNA",
                                IRanges(start=round(runif(100)*100),
                                width=round(runif(100)*100+1)), strand="+",
                                EUC=round(runif(100)*100))
dummy_comp_GR_control <- comp(dummy_euc_GR_control)
dummy_comp_GR_treated <- comp(dummy_euc_GR_treated)
dummy_norm <- dtcr(control_GR=dummy_comp_GR_control,
                   treated_GR=dummy_comp_GR_treated)
write(strwrap("chr1\t134212702\t134229870\tDummyRNA\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")
norm2bedgraph(norm_GR = dummy_norm, bed_file = "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)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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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/norm2bedgraph.Rd_%03d_medium.png", width=480, height=480)
> ### Name: norm2bedgraph
> ### Title: Exporting data in norm_df data frame (product of dtcr, slograt
> ###   and swinsor) to bedgraph format compatible with UCSC Genome Browser
> ### Aliases: norm2bedgraph
> 
> ### ** Examples
> 
> dummy_euc_GR_control <- GRanges(seqnames="DummyRNA",
+                                  IRanges(start=round(runif(100)*100),
+                                  width=round(runif(100)*100+1)), strand="+",
+                                  EUC=round(runif(100)*100))
> dummy_euc_GR_treated <- GRanges(seqnames="DummyRNA",
+                                 IRanges(start=round(runif(100)*100),
+                                 width=round(runif(100)*100+1)), strand="+",
+                                 EUC=round(runif(100)*100))
> dummy_comp_GR_control <- comp(dummy_euc_GR_control)
Fasta file not specified.
0 % of EUCs removed due to cutoff
> dummy_comp_GR_treated <- comp(dummy_euc_GR_treated)
Fasta file not specified.
0 % of EUCs removed due to cutoff
> dummy_norm <- dtcr(control_GR=dummy_comp_GR_control,
+                    treated_GR=dummy_comp_GR_treated)
> write(strwrap("chr1\t134212702\t134229870\tDummyRNA\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")
> norm2bedgraph(norm_GR = dummy_norm, bed_file = "dummy.bed")
Warning: normalization method to convert not specified. dtcr chosen.
Warning message:
Using togroup() on a CompressedIRangesList object is deprecated. Please
  use togroup(PartitioningByWidth(...)) instead. 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>