dtcr: Calculate deltaTCR.

In RNAprobR: An R package for analysis of massive parallel sequencing based RNA structure probing data

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.

See Also

comp, slograt, swinsor, compdata, GR2norm_df, plotRNA, 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)
dummy_comp_GR_treated <- comp(dummy_euc_GR_treated)
dtcr(control_GR=dummy_comp_GR_control, treated_GR=dummy_comp_GR_treated)

RNAprobR documentation built on Nov. 8, 2020, 5:57 p.m.