haploReconstruct (version 0.1.2)

inspect_window_dbScan,hbr-method: Clustering with the dbscan algorithm

Description

Performs clustering with the dbscan (Density-based spatial clustering of applications with noise) for all SNPs in a window after filtering (i.e. initialize_SNP_time_series) and visualizes found clusters based on principal components. NOTE: The clusters identified here are not nessesarily identical with the clusters identified with average linkage clustering. Therefore if haplotype reconstruction was done using average linkage clustering the clusters shown here can be different from clusters of identified haplotype blocks.

Usage

"inspect_window_dbScan"(object, window, minPts = [e-mail], eps, plotkNN = 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

minPts

Number of minimum points in the eps region (for core points). (default min.cl.size used for haplotype block reconstruction)

eps

The size of the epsilon neighborhood. Defines the distance between samples that built up a core cluster, for details see ?dbscan of the dbscan package. (This value is only used for the plotCluster functionality.)

plotkNN

Boolean indicating if the kNN distance plot should be printed , for details see ?kNNdistplot of the dbscan package. Briefly, the y-value where a bent in the curve is visible is a good indicator of the eps value to choose for the given k = minPts.

plotCluster

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

Details

Performs clustering with dbscan (Density-based spatial clustering of applications with noise) for all SNPs in a window after filtering (i.e. initialize_SNP_time_series) and visualizes found clusters based on principal components. NOTE: The clusters identified here are not nessesarily identical with the clusters identified with average linkage clustering. Therefore if haplotype reconstruction was done using average linkage clustering the clusters shown here can be different from clusters of identified haplotype blocks. This method is rather indendet for inspection and getting an idea if haplotype reconstruction should rather be run using dbscan instead of average linkage clustering.

This package used the dbscan implementation of the package dbscan (Michael Hahsler) originally described by Ester et al. (1996).

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_avLink number_hbr