linkage.blocks.network:
Calculates linkage blocks using community detection.
Description
This function calculates linkage blocks based on correlation between markers on a single chromosome. A correlation matrix is converted to a weighted adjacency matrix, and the fastgreedy community detection algorithm from R/igraph is used to define linkage blocks. Adjacent markers in the same community are grouped into a single linkage block.
The object in which all results are stored. See read.population.
geno.obj
The object in which the genotype matrix and marker information are stored. See read.geno.
collapse.linked.markers
A logical value indicating whether markers should be collapsed into linkage blocks or treated separately.
threshold.power
A value for soft-thresholding the marker-marker correlation matrix before community detection is run.
plot.blocks
A logical value indicating whether the blocks should be plotted. If TRUE, a pdf titled "Recomb.Images.Genotype.Net.Thresh.X.pdf" is generated, where X indicates the soft-thresholding power.
Value
Returns the data object with a new element called linkage.blocks.collapsed if collapse.linked.markers is TRUE, and linkage.blocks.full if collapse.linked.markers is FALSE.
References
Csardi G, Nepusz T: The igraph software package for complex network research, InterJournal, Complex Systems 1695. 2006. http://igraph.org