swinsor: Smooth Winsorization

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/swinsor.R

Description

Performs sliding window Winsorization given treated GRanges generated by comp() function. It winsorizes values in windows (of a size specified by window_size) sliding by 1 nt over whole transcript length and reports mean winsorized value for each nucleotide (as well as standard deviation).

Usage

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swinsor(Comp_GR, winsor_level = 0.9, window_size = 71, only_top = FALSE,
  nt_offset = 1, add_to)

Arguments

Comp_GR

GRanges object made by comp() function.

winsor_level

Winsorization level. Bottom outliers will be set to (1-winsor_level)/2 quantile and top outliers to (1+winsor_level)/2 quantile.

window_size

Size of a sliding window.

only_top

If TRUE then bottom values are not Winsorized and are set to 0.

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.

add_to

GRanges object made by other normalization function (dtcr(), slograt(), swinsor(), compdata()) to which normalized values should be added.

Value

GRanges object with "swinsor" (mean smooth-Winsor values) and "swinsor.sd" (standard deviation of smooth-Winsor values) metadata.

Author(s)

Lukasz Jan Kielpinski, Jeppe Vinther, Nikos Sidiropoulos

References

"Analysis of sequencing based RNA structure probing data" Kielpinski, Sidiropoulos, Vinther. Chapter in "Methods in Enzymology" (in preparation)

See Also

comp, dtcr, slograt, compdata, GR2norm_df, plotRNA, norm2bedgraph, winsor, swinsor_vector

Examples

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

RNAprobR documentation built on May 31, 2017, 10:52 a.m.