ACO: Aggregation of Circular Orders
In isocir: Isotonic Inference for Circular Data

ACO	R Documentation

Aggregation of Circular Orders

Description

This function computes the aggregation of circular orders.

Usage

ACO(data, method=c("Naive", "CB", "CMC", "TSP", "CH"), 
control.method, ws=NULL, coef=1)

Arguments

`data`	vector or matrix of data to be processed. See details.
`method`	"Naive", "CB", "CMC", "TSP", "CH".
`control.method`	"tau", "MSCE", "pos", "cirmean", "cirmed", "1", "2", "3", "4m", "4c", "bin", "pos", "alpha1", "alpha2", "alpha3", "alpha4","alphainf", "time", "arc", "chord", "bin", "pos", "cos", "cmean", "mrl", "e3", "ave", "qua", "nat", "natp", "natb".
`ws`	the weights.
`coef`	The coeficient for TSP method.

Details

This function computes the aggregation of circular orders.

The possible methods are: Naive: the naive method of choosing the order from the data. CB: the circular Borda method. TSP: the Traveling Salesperson Problem apply to aggregation of circular orders. CH: the circular Hodge method.

The coef argument is the proportion of maximum presolutions check respect to the number of elements n. It means that when the TSP is solved by heuristics, a maximum of the best coef*n possible solutions are proned to be the final solution, they are checked and the one with the best SCE is chosen.

Value

A list with the elements:

`aggre_order`	the circular aggregated order.
`msce`	the MSCE corresponding to the circular aggregated order.
`mtau`	the circular Kendall tau corresponding to the circular aggregated order.
`mintour`	the order corresponding to the tour of minimum length in case of TSP.
`mt_msce`	in case of TSP, the MSCE corresponding to the tour of minimum length.
`tour_length`	in case of TSP, the length of the tour.
`scores`	in case of TSP, the length of each edge. In case of circular Hodge, the scores.
`out`	in case of circular Hodge, the element where the circle is cut.
`error1`	in case of circular Hodge method, the error1.
`error2`	in case of circular Hodge method, the error2.

Author(s)

Author(s): Sandra Barragán. Maintainer: <sandra.barragan@gmail.com>

References

Rueda, C., Fernandez, M. A. and Peddada, S. D. (2009). Estimation of parameters subject to order restrictions on a circle with application to estimation of phase angles of cell-cycle genes. Journal of the American Statistical Association, 104, n485; pp 338–347. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2742472/

Fernandez, M. A., Rueda, C. and Peddada, S. D. (2012). Identification of a core set of signature cell cycle genes whose relative order of time to peak expression is conserved across species, Nucl. Acids Res. 40, n7: pp 2823–2832. doi:10.1093/nar/gkr1077. https://academic.oup.com/nar/article/40/7/2823/1183140

Barragan, S., Rueda, C., Fernandez, M.A. and Peddada, S.D. (2015). Determination of Temporal Order among the Components of an Oscillatory System. PLOS ONE. 10, n7: pp 1–14. doi: 10.1371/journal.pone.0124842. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4495067/

Examples

data(cirgenes)
ACO(cirgenes[,c(1:5)], method="TSP", control.method="alpha3")
#datos<- rbind (c(0, 1/10, 1/9, 1, 11/10, 10/9)*pi,c(0, 1/2, 1/10, 1, 3/2, 11/10)*pi) 
#ACO(datos, method="TSP", control.method="alpha3")

isocir documentation built on Aug. 17, 2023, 9:07 a.m.