graph.params2symbolic.fstats: Provide a symbolic representation of all the F-statistics and...

In poolfstat: Computing f-Statistics and Building Admixture Graphs Based on Allele Count or Pool-Seq Read Count Data

Provide a symbolic representation of all the F-statistics and the model system of equations

Description

Provide a symbolic representation of all the F-statistics and the model system of equations

Usage

graph.params2symbolic.fstats(x, outfile = NULL)

Arguments

x	An object of class graph.params containing graph information and relevant Fstats estimates (see the function generate.graph.params)
outfile	The file where to print the equations (default=NULL, equations are not printed in a file)

Value

A list with the following elements:

1. "model.matrix": A symbolic representation of the matrix M relating the basis F-statistics and graph edge length as F=M*b where F is the vector of the basis Fstats (row names of model.matrix M) and b is the vector of graph edges (column names of model.matrix M).

2. "omega": A symbolic representation of the scaled covariance matrix of allele frequency with edge names and admixture parameter names as specified in the edges.names and adm.params.names slot of the input graph.params object x

3. "F2.equations": A symbolic representation of the nleaves(nleaves-1)/2 different F2 as a function of graph parameters

4. "F3.equations": A symbolic representation of the nleaves(nleaves-1)(nleaves-2)/2 different F3 as a function of graph parameters

5. "F4.equations": A symbolic representation of the npops(npops-1)(npops-2)(npops-3)/8 different F4 as a function of graph parameters

See Also

To generate a graph.params object, see generate.graph.params.

Examples

graph=rbind(c("P1","P7",""),c("P2","s1",""),c("P3","s2",""),c("P6","S",""),
            c("S","s1","a"),c("S","s2","(1-a)"),c("s2","P8",""),c("s1","P7",""),
            c("P4","P9",""),c("P5","P9",""),c("P7","P8",""),
            c("P8","R",""),c("P9","R","")) 
graph.params=generate.graph.params(graph)
graph.equations=graph.params2symbolic.fstats(graph.params) 

poolfstat documentation built on Sept. 8, 2023, 5:49 p.m.