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Last data update: 2014.03.03

R: Calculate deltaTCR.

dtcr	R Documentation

Calculate deltaTCR.

Description

Performs deltaTCR (dtcr) normalization given control and treated GRanges generated by comp() function.

Usage

dtcr(control_GR, treated_GR, window_size = 3, nt_offset = 1,
  bring_to_zero = TRUE, add_to)

Arguments

`control_GR`	GRanges object made by comp() function from the control sample.
`treated_GR`	GRanges object made by comp() function from the treated sample.
`window_size`	if smoothing is to be performed, what should be the window size? (use only odd numbers to ensure that windows are centred on a nucleotide of interest) (default: 3)
`nt_offset`	how many nucleotides before a modification the reverse transcription terminates. E.g. for HRF-Seq nt_offset=1 (default: 1)
`bring_to_zero`	should in deltaTCR calculations negative deltaTCR's be brought to 0 as was done in HRF-Seq paper (default: T)
`add_to`	GRanges object made by other normalization function (dtcr(), slograt(), swinsor(), compdata()) to which normalized values should be added.

Value

GRanges object with "dtcr" (deltaTCR) and "dtcr.p" (p.value of comparing control and treated calcualted with pooled two-proportion Z-test) metadata.

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.

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)
dtcr(control_GR=dummy_comp_GR_control, treated_GR=dummy_comp_GR_treated)

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/dtcr.Rd_%03d_medium.png", width=480, height=480)
> ### Name: dtcr
> ### Title: Calculate deltaTCR.
> ### Aliases: dtcr
> 
> ### ** 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
> dtcr(control_GR=dummy_comp_GR_control, treated_GR=dummy_comp_GR_treated)
GRanges object with 182 ranges and 3 metadata columns:
        seqnames     ranges strand |        nt               dtcr
           <Rle>  <IRanges>  <Rle> | <numeric>          <numeric>
    [1] DummyRNA     [1, 1]      + |         0  0.333333333333333
    [2] DummyRNA     [2, 2]      + |         0                  0
    [3] DummyRNA     [3, 3]      + |         0                  0
    [4] DummyRNA     [4, 4]      + |         0 0.0203582410296858
    [5] DummyRNA     [5, 5]      + |         0 0.0338641712022826
    ...      ...        ...    ... .       ...                ...
  [178] DummyRNA [178, 178]      + |         0                  0
  [179] DummyRNA [179, 179]      + |         0                  0
  [180] DummyRNA [180, 180]      + |         0                  0
  [181] DummyRNA [181, 181]      + |         0                  0
  [182] DummyRNA [182, 182]      + |         0                  0
                      dtcr.p
                   <numeric>
    [1]    0.946285489169598
    [2] 1.10131528823137e-50
    [3] 3.86254699316696e-29
    [4] 6.39489643371974e-07
    [5]    0.797650810147084
    ...                  ...
  [178]                 <NA>
  [179]                 <NA>
  [180]                 <NA>
  [181]                 <NA>
  [182]                 <NA>
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>