GR2norm_df: Export normalized GRanges object to data frame

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

Description

Function to make data frame out of GRanges output of normalizing functions (dtcr(), slograt(), swinsor(), compdata()) for all or a set of chosen transcripts in the file.

Usage

GR2norm_df(norm_GR, RNAid = "all", norm_methods = "all")

Arguments

norm_GR	GRanges object made by other normalization function (dtcr(), slograt(), swinsor(), compdata()) from which data is to be extracted
RNAid	Transcript identifiers of transcripts that are to be extracted
norm_methods	Names of the columns to be extracted.

Value

Data frame object with columns: RNAid, Pos and desired metadata columns (e.g. nt, dtcr)

Author(s)

Lukasz Jan Kielpinski, Nikos Sidiropoulos

See Also

norm_df2GR, dtcr, swinsor, slograt, compdata

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)
GR2norm_df(dummy_swinsor)

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