PQSViews {pqsfinder}R Documentation

PQSViews class constructor

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)


[Package pqsfinder version 2.10.1 Index]