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Last data update: 2014.03.03

R: Import bedgraph to GRanges

bedgraph2norm

R Documentation

Import bedgraph to GRanges

Description

Function importing data from bedgraph format compatible with UCSC Genome Browser to norm_GR data frame. Warning: Compatible only with bedgraph files generated by norm2bedgraph function (bedgraph needs to have 2 tracks, first for plus strand, second for minus strand). May be used for transforming normalized data to another different annotation sets.

Usage

bedgraph2norm(bedgraph_file, fasta_file, txDb, bed_file,
  column_name = "bedgraph_score", add_to, track_strand = "+")

Arguments

`bedgraph_file`	path to compatible bedgraph file
`fasta_file`	path to fasta file which is used for a) choosing which transcripts to use (transcripts absent from fasta are not reported), b) providing sequence for to display in GRanges metadata
`txDb`	TranscriptDb object with transcript definitions. Names must match those in fasta_file
`bed_file`	character containing file path to BED file with transcript definitions. Supply txDb XOR bedfile
`column_name`	How to name imported metadata in GRanges
`add_to`	GRanges object made by other normalization function (dtcr(), slograt(), swinsor(), compdata()) to which values from bedgraph should be added.
`track_strand`	specifies which genomic strand the supplied bedgraph describes ("+" or "-"). Used only if the bedgraph file is composed of only one track.

Value

Function creates GRanges object or (if add_to specified) adds metadata to already existing object

Author(s)

Lukasz Jan Kielpinski, Nikos Sidiropoulos

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")

write(c(">DummyRNA", paste(sample(c("A","C","G","T"), 100, replace=TRUE),
                           collapse="")), file="dummy.fa")
bedgraph2norm(bedgraph_file = "out_file.bedgraph", fasta_file = "dummy.fa",
              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
'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/bedgraph2norm.Rd_%03d_medium.png", width=480, height=480)
> ### Name: bedgraph2norm
> ### Title: Import bedgraph to GRanges
> ### Aliases: bedgraph2norm
> 
> ### ** 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. 
> 
> write(c(">DummyRNA", paste(sample(c("A","C","G","T"), 100, replace=TRUE),
+                            collapse="")), file="dummy.fa")
> bedgraph2norm(bedgraph_file = "out_file.bedgraph", fasta_file = "dummy.fa",
+               bed_file = "dummy.bed")
For RNA  DummyRNA positions outside FASTA annotation exist. N's added
GRanges object with 189 ranges and 2 metadata columns:
               seqnames     ranges strand |          nt bedgraph_score
                  <Rle>  <IRanges>  <Rle> | <character>      <numeric>
    DummyRNA.1 DummyRNA     [1, 1]      + |           C      0.3333333
    DummyRNA.2 DummyRNA     [2, 2]      + |           A      0.5460317
    DummyRNA.3 DummyRNA     [3, 3]      + |           A      0.3342521
    DummyRNA.4 DummyRNA     [4, 4]      + |           A      0.3757211
    DummyRNA.5 DummyRNA     [5, 5]      + |           T      0.2265148
           ...      ...        ...    ... .         ...            ...
  DummyRNA.185 DummyRNA [185, 185]      + |           N              0
  DummyRNA.186 DummyRNA [186, 186]      + |           N              0
  DummyRNA.187 DummyRNA [187, 187]      + |           N              0
  DummyRNA.188 DummyRNA [188, 188]      + |           N              0
  DummyRNA.189 DummyRNA [189, 189]      + |           N              0
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
Warning messages:
1: In asMethod(object) : NAs introduced by coercion
2: Using togroup() on a CompressedIRangesList object is deprecated. Please
  use togroup(PartitioningByWidth(...)) instead. 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>