comp {RNAprobR} | R Documentation |
comp() takes as input euc_GR GRanges object produced by readsamples() and produces Comp_GR GRanges.
comp(euc_GR, cutoff = 1, fasta_file)
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) |
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.
Lukasz Jan Kielpinski, Nikos Sidiropoulos
Kielpinski, L.J., and Vinther, J. (2014). Massive parallel-sequencing-based hydroxyl radical probing of RNA accessibility. Nucleic Acids Res.
readsamples
, dtcr
,
slograt
, swinsor
, compdata
,
comp
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)