find.points {seq2R} | R Documentation |
Simple method to detect compositional changes in genomic sequences
Description
find
is used to detect changes at genomic sequences composition. The method is based on fitting nonparametric models by using local linear kernel smoothers.
Usage
find.points(x,kbin= 300, p= 3, bandwidth=-1, weights= 1, nboot=100, kernel="gaussian",
n.bandwidths= 20, seed = NULL, ...)
Arguments
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. |
Details
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)
.
Value
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. |
Author(s)
Nora M. Villanueva and Marta Sestelo.
References
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.
Examples
library(seq2R)
#mtDNAhum <- read.genbank("NC_012920")
data(mtDNAhum)
DNA <- transform(mtDNAhum)
seq1<-find.points(DNA)
seq1