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 2.8.0 Index]