PQSViews {pqsfinder} | R Documentation |
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.
PQSViews(subject, start, width, strand, score, density, max_scores, nt, nb, nm, rl1, rl2, rl3, ll1, ll2, ll3)
subject |
DNAString object. |
start |
Start positions. |
width |
Lengths. |
strand |
Strand specifications. |
score |
Scores. |
density |
Numbers of PQS overlapping at each position in |
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. |
Use elementMetadata
function to get extra PQS features
like number of tetrads, bulges, mismatches or loop lengths.
PQSViews object.
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)