haploReconstruct (version 0.1.2)

inspect_window_avLink,hbr-method: Hierachical clustering of haplotype-block marker for a window

Description

Performs average linkage clustering for all SNPs in a window after filtering (i.e. initialize_SNP_time_series).

Usage

"inspect_window_avLink"(object, window, min.cl.cor = 0, plotDendro = T, plotCluster = T)

Arguments

object

object of class hbr containing the results of reconstructed haplotype-blocks

window

number of the window, which should be inspected

min.cl.cor

minimum cluster correlation, if none is provided, the min.cl.cor of the provided hbr object is taken.

plotDendro

Boolean indicating if dendrogram using average linkage clustering should be plotted.

plotCluster

Boolean indicating if clusters identified with average linkage clustering should be visualized in PCs.

Details

Performs average linkage clustering on the time series data of the filtered SNPs and the selected time points (filtered and selected through use.libs in initialize_SNP_time_series) in a given window. The horizontal red line indicates the correlation (1-correlation) threshold on which clusters were originally identified. Note: Clusters with less than min.cl.cor markers are discarded. If no horizontal line is shown this indicates that all SNPs were assigned to the same cluster.

See Also

hbr ex_dat summary.hbr plot.hbr plot_cluster_trajectories plot_marker_trajectories map rev_map markers plot_hbr_freq inspect_window inspect_window_PCA inspect_window_dbScan number_hbr