inspect_window_PCA-hbr-method: PCA of haplotype-block marker for a window

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

Description

Plots all filtered SNPs for a given window in terms of their the first two principal components of the respective time series data.

Usage

## S4 method for signature 'hbr'
inspect_window_PCA(object, window)

Arguments

object	object of class hbr containing the results of reconstructed haplotype-blocks
window	number of the window, which should be inspected

Details

Performs principal component analysis (PCA) 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. SNPs are shown in terms of the first two principal components and colored according to the haplotype-block they were assigned to. Black colored points were not assigned to any 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_avLink inspect_window_dbScan number_hbr

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