GiGList.Updater: Analysis Updater for a G4-iM Grinder List (GiGList)

In EfresBR/G4iMGrinder: G4iMGrinder: G4 Quadruplex, i-Motif and higher-order structures in DNA and RNA sequences search and analysis tool.

Description

A function that can be used to update the results of G4-iM Grinder List with different a variable configuration. Allows the complete analytic potential on existing results (except cGcC). Allows detection of opposite base-pair quadruplex structures on the opposite strand, avoiding all together a new quadruplex search [it is more efficient than a new G4-iM Grinder analysis].

Usage

G4iMGrinder::GiGList.Updater(GiG.List, RunComposition = "G", LoopSeq = c("G", "T", "A", "C"), G4hunter = TRUE, PQSfinder = TRUE, Bt = 14, Pb = 17, Fm = 3, Em = 1, Ts = 4, Et = 1, Is = -19, Ei = 1, Ls = -16, ET = 1, WeightParameters = c(50, 50, 0), FreqWeight = 0, KnownQuadruplex = TRUE, KnownNOTQuadruplex = FALSE, NCores = 1 )

Arguments

GiGList	list, G4-iM Grinder results in the form of a GiGList
ChangeRunComposition	logical, allows the detection of opposite base-pair quadruplex structures. Predefined values is FALSE.
...	Rest of items can be found in the G4iMGrinder documentation. These values are all set to predefined values as in G4-iM Grinder

Value

The result of the function is a GiGList with the new analysis.

Author(s)

Efres Belmonte-Reche

Examples

  # Creating the G4iMGrinder Results for the DNA search of G-quadruplex.
  Rs.G4 <- G4iMGrinder(Name = Name, Sequence = Sequence)

  # Finding the potential i-Motifs using the previous analysis,  and including known NOT quadruplex structures (by default OFF).
  Rs.iM <- GiGList.Updater(Rs.G4, ChangeRunComposition = TRUE, KnownNotQuadruplex = TRUE)

  # Changing score weights and frequency importance in calculations of Final Score
  Rs.iMScores <- GiGList.Updater(Rs.iM, WeightParameters = c(100, 50, 0), FreqWeight = 50)

EfresBR/G4iMGrinder documentation built on June 11, 2021, 2:57 a.m.