find.points {seq2R} | R Documentation |
find
is used to detect changes at genomic sequences composition. The method is based on fitting nonparametric models by using local linear kernel smoothers.
find.points(x,kbin= 300, p= 3, bandwidth=-1, weights= 1, nboot=100, kernel="gaussian",
n.bandwidths= 20, seed = NULL, ...)
x |
Sequences in binary system (by using |
kbin |
The number of binning nodes over which the function is to be estimated. |
p |
Degree of the polynomial. By default |
bandwidth |
The kernel bandwidth or smoothing parameter. Large values of bandwidth make smoother estimates, smaller values of bandwidth make less smooth estimates. The default |
weights |
Weights. |
nboot |
Number of bootstrap repeats. |
kernel |
Character which denotes the kernel function (a symmetric density). By default |
n.bandwidths |
Number that it will be used to calculate the grid of bandwidths in a range between 0 and 1. In this grid, it will be selected the optimum bandwidth by cross-validation.If the optimum bandwidth value is close to 0, we will obtain rough estimates; when it is close to 1, we will obtain smooth estimates. |
seed |
Seed to be used in the bootstrap procedure. |
... |
Other options. |
For each genomic sequence the AT and CG skews profiles were calculated as A vs. T = (A-T)/(A+T)
and C vs. G = (C-G)/(C+G)
.
The function computes and returns a list of short information for a fitted change.points
object.
Number of A-T base pairs |
The returned value is the total nucleotide (adenine and thymine) contained at the sequence analyzed. |
Number of C-G base pairs |
In this case, the returned value is the sum of cytosine and guanine contained at the sequence. |
Number of binning nodes |
The number of binning nodes over which the function is to be estimated. |
Number of bootstrap repeats |
Number of bootstrap repeats. |
Bandwidth |
Value of the kernel bandwidth or smoothing parameter used in the fitting for A vs. T and C vs. G. |
Exists any critical point |
Emphasize if there is or not any critical. |
Nora M. Villanueva and Marta Sestelo.
N. M. Villanueva, M. Sestelo, M. M. Fonseca and J. Roca-Pardinas (2023). seq2R: An R package to detect change points in DNA sequences. Mathematics, 11 (10), 2299.
library(seq2R)
#mtDNAhum <- read.genbank("NC_012920")
data(mtDNAhum)
DNA <- transform(mtDNAhum)
seq1<-find.points(DNA)
seq1