Create or extend norm_GR GRanges using Comp_GR GRanges

Description

Add metadata present in GRanges made by comp() function (termination count (TC), termination-coverage ratio (TCR), coverage (Cover) and priming count (PC)) to GRanges made by normalizing functions (dtcr(), slograt(), swinsor(), compdata()).

Usage

compdata(Comp_GR, nt_offset = 1, add_to)

Arguments

Value

Author(s)

Lukasz Jan Kielpinski, Nikos Sidiropoulos

See Also

comp, dtcr, slograt, swinsor, GR2norm_df, plotRNA, norm2bedgraph

Examples

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_treated <- comp(dummy_euc_GR_treated)
dummy_swinsor <- swinsor(dummy_comp_GR_treated)
dummy_swinsor <- compdata(Comp_GR=dummy_comp_GR_treated,
                          add_to=dummy_swinsor)
dummy_swinsor

Results

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/compdata.Rd_%03d_medium.png", width=480, height=480)
> ### Name: compdata
> ### Title: Create or extend norm_GR GRanges using Comp_GR GRanges
> ### Aliases: compdata
> 
> ### ** Examples
> 
> 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_treated <- comp(dummy_euc_GR_treated)
Fasta file not specified.
0 % of EUCs removed due to cutoff
> dummy_swinsor <- swinsor(dummy_comp_GR_treated)
> dummy_swinsor <- compdata(Comp_GR=dummy_comp_GR_treated,
+                           add_to=dummy_swinsor)
> dummy_swinsor
GRanges object with 195 ranges and 7 metadata columns:
        seqnames     ranges strand |        nt   swinsor swinsor.sd        TC
           <Rle>  <IRanges>  <Rle> | <numeric> <numeric>  <numeric> <numeric>
    [1] DummyRNA     [1, 1]      + |         0         0          0         0
    [2] DummyRNA     [2, 2]      + |         0   0.29375          0        47
    [3] DummyRNA     [3, 3]      + |         0         0          0         0
    [4] DummyRNA     [4, 4]      + |         0    0.2625          0        42
    [5] DummyRNA     [5, 5]      + |         0   0.14375          0        23
    ...      ...        ...    ... .       ...       ...        ...       ...
  [191] DummyRNA [191, 191]      + |         0      <NA>       <NA>         0
  [192] DummyRNA [192, 192]      + |         0      <NA>       <NA>         0
  [193] DummyRNA [193, 193]      + |         0      <NA>       <NA>         0
  [194] DummyRNA [194, 194]      + |         0      <NA>       <NA>         0
  [195] DummyRNA [195, 195]      + |         0      <NA>       <NA>         0
                       TCR     Cover        PC
                 <numeric> <numeric> <numeric>
    [1]                  0       174         0
    [2]  0.212669683257919       221         0
    [3]                  0       221         0
    [4]  0.159695817490494       263         0
    [5] 0.0804195804195804       286         0
    ...                ...       ...       ...
  [191]                  0        99         0
  [192]                  0        99         0
  [193]                  0        99        88
  [194]                  0        11         0
  [195]                  0        11        11
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>