linkage_blocks_network: Identify linkage blocks

In cape: Combined Analysis of Pleiotropy and Epistasis for Diversity Outbred Mice

Identify linkage blocks

Description

This function identifies linkage blocks among markers using pairwise correlation between genotypes. The algorithm clusters adjacent, correlated markers using the fastgreedy community detection algorithm from R/igraph

Usage

linkage_blocks_network(
  data_obj,
  geno_obj,
  collapse_linked_markers = TRUE,
  threshold_power = 1,
  plot_blocks = TRUE
)

Arguments

data_obj	a Cape object
geno_obj	a genotype object
collapse_linked_markers	A logical value. If TRUE markers are combined into linkage blocks based on correlation. If FALSE, each marker is treated as an independent observation.
threshold_power	A soft threshold power. The marker correlation matrix is raised to this power to increase or decrease the number of linkage blocks detected. Increasing the power makes more linkage blocks, and decreasing the power makes fewer linkage blocks. The default power is 1, which uses the correlation matrix as is.
plot_blocks	logical. If TRUE, the marker correlation matrices are plotted and the boundaries of the blocks are shown.

Details

Csardi G, Nepusz T: The igraph software package for complex network research, InterJournal, Complex Systems 1695. 2006. https://igraph.org

The correlation network can be optionally soft thresholded to increase or decrease resolution.

Value

The data object is returned with a new list called linkage_blocks_collapsed if collapse_linked_markers is TRUE and linkage_blocks_full if collapse_linked_markers is FALSE Each element of the list is one linkage block and contains a vector naming the markers in that block. Blocks are named with a chromosome number and an index.

cape documentation built on May 29, 2024, 5:11 a.m.