eq.test {isocir} | R Documentation |
Test of Equality of Circular Orders
Description
This function calculates the test of equality of circular orders in different populations.
Usage
eq.test(data, popu, ws=NULL, method=NULL, control.method=NULL, output=NULL, coef=1, N=500)
Arguments
data |
matrix or data.frame with the data. See details. |
popu |
a numeric vector with population to each experiment belongs. |
ws |
a numeric vector with the values to be used as weight per experiment. |
method |
The method to be used to aggregate circular orders with ACO function. |
control.method |
The argument to control the method in ACO function. |
output |
The path where write the output of the global orders. |
coef |
The coefficient to use in case of method=TSP, by default 1. |
N |
The number of randomization selections, by default 500. |
Details
This function performs the test to constrast equality of circular orders:
The circular parameters follow the same circular order in all populations.
is not true.
The data
must have the elements in the columns and the experiments in the rows.
Value
The output is a list with the following values:
allorders |
matrix, in each row the circular order obtained with all selected experiments and the value for the statistic test in that selection. |
pvalue |
numeric, it is the p-value what results of the test. |
global_order |
numeric vector with the elements ordered as the global circular order estimate. |
CC |
numeric, the confidence coefficient (in percentage) of the global order. |
MFO |
numeric vector with the elements ordered as the Most Frequent global Order in the randomization procedure. |
CCMFO |
numeric, the confidence coefficient (in percentage) of the Most Frequent global Order. |
Two additional outputs could be obtained in the form of .csv files written in the path given by the user in the argument output
:
globalorders.csv |
all the global orders obtained from the randomization procedure and the value of the statistic in each selection. |
frequencydist.csv |
the frequency distribution of all the global orders. |
Author(s)
Author(s): Sandra Barrag?n. 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/
See Also
ACO
, CIRE
,sce
, mrl
, isocir
, plot.isocir
.
Examples
data(cirgenes)
eq.test(cirgenes[-8,c(1:5)], popu=c(rep(1,5),rep(2,4)),
ws=c(1,2,3.5,2,1,8,4.2,1.35,6), method="TSP",control.method="alpha3",N=2)