PQSViews: PQSViews class constructor

Description Usage Arguments Details Value Examples

View source: R/PQSViews-class.R

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

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

Arguments

subject

DNAString 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

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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. 1, 2018, 4:28 a.m.