PQSViews: PQSViews class constructor

In pqsfinder: Identification of potential quadruplex forming sequences

Description

User friendly constructor for PQSViews class representing potential quadruplex forming sequences (PQS). PQSViews is a subclass of XStringViews class and adds two more slots to store PQS density and PQS score distribution.

Usage

PQSViews(subject, start, width, strand, score, density, max_scores, nt, nb,
  nm, rl1, rl2, rl3, ll1, ll2, ll3)

Arguments

subject	DNAString or RNAString object.
start	Start positions.
width	Lengths.
strand	Strand specifications.
score	Scores.
density	Numbers of PQS overlapping at each position in subject.
max_scores	Score of the best PQS found at each position.
nt	Tetrad numbers.
nb	Bulge counts.
nm	Mismatch counts.
rl1	Run 1 lengths.
rl2	Run 2 lengths.
rl3	Run 3 lengths.
ll1	Loop 1 lengths.
ll2	Loop 2 lengths.
ll3	Loop 3 lengths.

Details

Use elementMetadata function to get extra PQS features like number of tetrads, bulges, mismatches or loop lengths.

Value

PQSViews object.

Examples

pv <- PQSViews(DNAString("GGTGGTGGTGG"), 1, 11, "+", 33, as.integer(rep(1, 11)),
               as.integer(rep(33, 11)), 2, 0, 0, 2, 2, 2, 1, 1, 1)
start(pv)
width(pv)
strand(pv)
score(pv)
density(pv)
maxScores(pv)
elementMetadata(pv)

pqsfinder documentation built on Nov. 8, 2020, 5:52 p.m.