GR2norm_df: Export normalized GRanges object to data frame

Description Usage Arguments Value Author(s) See Also Examples

View source: R/auxiliary_functions.R

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

1
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

1
2
3
4
5
6
7
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)

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