dtcr {RNAprobR} | R Documentation |
Performs deltaTCR (dtcr) normalization given control and treated GRanges generated by comp() function.
dtcr(control_GR, treated_GR, window_size = 3, nt_offset = 1, bring_to_zero = TRUE, add_to)
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. |
GRanges object with "dtcr" (deltaTCR) and "dtcr.p" (p.value of comparing control and treated calcualted with pooled two-proportion Z-test) metadata.
Lukasz Jan Kielpinski, Nikos Sidiropoulos
Kielpinski, L.J., and Vinther, J. (2014). Massive parallel-sequencing-based hydroxyl radical probing of RNA accessibility. Nucleic Acids Res.
comp
, slograt
, swinsor
,
compdata
, GR2norm_df
, plotRNA
,
norm2bedgraph
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)