comp: Arranging information from GRanges produced by readsamples()...

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

Description

comp() takes as input euc_GR GRanges object produced by readsamples() and produces Comp_GR GRanges.

Usage

comp(euc_GR, cutoff = 1, fasta_file)

Arguments

euc_GR	GRanges generated by readsamples() function
cutoff	specifies cutoff length, only inserts of this length or longer will be used for processing (default: 1)
fasta_file	path to fasta file to which reads were mapped. Used to report nucleotide at each position (not required)

Value

GRanges object with: 1) seqnames (RNAid), 2) start (position within RNA), and metadata: 3) TCR (termination coverage ratio), 4) TC (termination count), 5) Cover (coverage) and 6) PC (priming count) for each position within each RNA.

Author(s)

Lukasz Jan Kielpinski, Nikos Sidiropoulos

References

Kielpinski, L.J., and Vinther, J. (2014). Massive parallel-sequencing-based hydroxyl radical probing of RNA accessibility. Nucleic Acids Res.

See Also

readsamples, dtcr, slograt, swinsor, compdata, comp

Examples

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

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