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

In haploReconstruct: Reconstruction of Haplotype-Blocks from Time Series Data

Description

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

Usage

## S4 method for signature 'hbr'
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.

Author(s)

Susanne U. Franssen

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

haploReconstruct documentation built on May 2, 2019, 1:46 p.m.