slograt: Smooth Log2-ratio

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

Description

Performs smooth-log2-ratio calculation given control and treated GRanges generated by comp() function.

Usage

slograt(control_GR, treated_GR, window_size = 5, nt_offset = 1,
  depth_correction = "all", pseudocount = 5, 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, then what should be the window size? (use only odd numbers to ensure that windows are centred on a nucleotide of interest) (default: 5)
nt_offset	How many position in the 5' direction should the signal be offset to account for the fact that reverse transcription termination occurs before site of modification.
depth_correction	One of three values: "no" - counts are used as given, "all" - counts from sample with higher total sum of EUCs are multiplied by sum of EUCs from sample with lower total sum of EUCs and divided by sum of EUCs from sample with higher EUC count (default), "RNA" as in "all" but on per RNA basis
pseudocount	What pseudocount should be added to each nucleotide prior to calculating log2 ratio (default: 5)
add_to	GRanges object made by other normalization function (dtcr(), slograt(), swinsor(), compdata()) to which normalized values should be added.

Value

GRanges object with "slograt" (smooth log2 ratio) and "slograt.p" (p.value of comparing control and treated) metadata.

Author(s)

Lukasz Jan Kielpinski, Nikos Sidiropoulos

References

Wan, Y., Qu, K., Zhang, Q.C., Flynn, R.A., Manor, O., Ouyang, Z., Zhang, J., Spitale, R.C., Snyder, M.P., Segal, E., et al. (2014). Landscape and variation of RNA secondary structure across the human transcriptome. Nature 505, 706-709.

See Also

comp, dtcr, compdata, swinsor, 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)
slograt(control_GR=dummy_comp_GR_control, treated_GR=dummy_comp_GR_treated)

sidiropoulos/RNAprobR-old documentation built on May 29, 2019, 9:58 p.m.