compdata: Create or extend norm_GR GRanges using Comp_GR GRanges

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

Description

Add metadata present in GRanges made by comp() function (termination count (TC), termination-coverage ratio (TCR), coverage (Cover) and priming count (PC)) to GRanges made by normalizing functions (dtcr(), slograt(), swinsor(), compdata()).

Usage

compdata(Comp_GR, nt_offset = 1, add_to)

Arguments

Comp_GR	GRanges object made by comp() function.
nt_offset	how many nucleotides before modification the reverse transcription terminates (default: 1)
add_to	normalized data frame with already performed normalization of another kind. Results will be merged

Value

norm_GR

norm_GR GRanges extended by metadata from Comp_GR

Author(s)

Lukasz Jan Kielpinski, Nikos Sidiropoulos

See Also

comp, dtcr, slograt, swinsor, GR2norm_df, plotRNA, norm2bedgraph

Examples

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_treated <- comp(dummy_euc_GR_treated)
dummy_swinsor <- swinsor(dummy_comp_GR_treated)
dummy_swinsor <- compdata(Comp_GR=dummy_comp_GR_treated,
                          add_to=dummy_swinsor)
dummy_swinsor

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