Arranging information from GRanges produced by readsamples() on per position (nucleotide) basis.

Description

comp() takes as input euc_GR GRanges object produced by readsamples() and produces Comp_GR GRanges.

Usage

comp(euc_GR, cutoff = 1, fasta_file)

Arguments

Value

GRanges object with: 1) seqnames (RNAid), 2) start (position within RNA), and metadata: 3) TCR (termination coverage ratio), 4) TC (termination count), 5) Cover (coverage) and 6) PC (priming count) for each position within each RNA.

Author(s)

Lukasz Jan Kielpinski, Nikos Sidiropoulos

References

Kielpinski, L.J., and Vinther, J. (2014). Massive parallel-sequencing-based hydroxyl radical probing of RNA accessibility. Nucleic Acids Res.

See Also

readsamples, dtcr, slograt, swinsor, compdata, comp

Examples

dummy_euc_GR <- GRanges(seqnames="DummyRNA",
                        IRanges(start=round(runif(100)*100),
                        width=round(runif(100)*100+1)), strand="+",
                        EUC=round(runif(100)*100))
comp(dummy_euc_GR)

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/comp.Rd_%03d_medium.png", width=480, height=480)
> ### Name: comp
> ### Title: Arranging information from GRanges produced by readsamples() on
> ###   per position (nucleotide) basis.
> ### Aliases: comp
> 
> ### ** Examples
> 
> dummy_euc_GR <- GRanges(seqnames="DummyRNA",
+                         IRanges(start=round(runif(100)*100),
+                         width=round(runif(100)*100+1)), strand="+",
+                         EUC=round(runif(100)*100))
> comp(dummy_euc_GR)
Fasta file not specified.
0 % of EUCs removed due to cutoff
GRanges object with 188 ranges and 5 metadata columns:
           seqnames     ranges strand |        TC               TCR     Cover
              <Rle>  <IRanges>  <Rle> | <numeric>         <numeric> <numeric>
  DummyRNA DummyRNA     [1, 1]      + |        97                 1        97
  DummyRNA DummyRNA     [2, 2]      + |        98 0.502564102564103       195
  DummyRNA DummyRNA     [3, 3]      + |         0                 0       195
  DummyRNA DummyRNA     [4, 4]      + |        66 0.252873563218391       261
  DummyRNA DummyRNA     [5, 5]      + |        75 0.223214285714286       336
       ...      ...        ...    ... .       ...               ...       ...
  DummyRNA DummyRNA [184, 184]      + |      <NA>              <NA>       117
  DummyRNA DummyRNA [185, 185]      + |      <NA>              <NA>       117
  DummyRNA DummyRNA [186, 186]      + |      <NA>              <NA>        17
  DummyRNA DummyRNA [187, 187]      + |      <NA>              <NA>        17
  DummyRNA DummyRNA [188, 188]      + |      <NA>              <NA>        17
                  PC        nt
           <numeric> <logical>
  DummyRNA         0      <NA>
  DummyRNA         0      <NA>
  DummyRNA         0      <NA>
  DummyRNA         0      <NA>
  DummyRNA        98      <NA>
       ...       ...       ...
  DummyRNA         0      <NA>
  DummyRNA       100      <NA>
  DummyRNA         0      <NA>
  DummyRNA         0      <NA>
  DummyRNA        17      <NA>
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>