RNAprobR (version 1.4.0)

comp: Arranging information from GRanges produced by readsamples() on per position (nucleotide) basis.

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.

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)