ACO {isocir}

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: <[e-mail]>

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/

See Also

eq.test, sce, cond.test, mrl, isocir, plot.isocir.

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")