# Reconstruction of Haplotype-Blocks from Time Series Data

## Documentation for package ‘haploReconstruct’ version 0.1.2

- DESCRIPTION file.

## Help Pages

ex_dat | Example data set
hbr | An S4 class storing results from haplotype-block reconstruction
hbr-class | An S4 class storing results from haplotype-block reconstruction
initialize_SNP_time_series | Initialization of time series data as input for haplotype reconstruction
inspect_window | Haplotype-block marker inspection for a window
inspect_window-method | Haplotype-block marker inspection for a window
inspect_window.hbr | Haplotype-block marker inspection for a window
inspect_window_avLink | Hierachical clustering of haplotype-block marker for a window
inspect_window_avLink-method | Hierachical clustering of haplotype-block marker for a window
inspect_window_avLink.hbr | Hierachical clustering of haplotype-block marker for a window
inspect_window_dbScan | Clustering with the dbscan algorithm
inspect_window_dbScan-method | Clustering with the dbscan algorithm
inspect_window_dbScan.hbr | Clustering with the dbscan algorithm
inspect_window_PCA | PCA of haplotype-block marker for a window
inspect_window_PCA-method | PCA of haplotype-block marker for a window
inspect_window_PCA.hbr | PCA of haplotype-block marker for a window
map | Map from reconstructed haplotype-blocks to windows
map-method | Map from reconstructed haplotype-blocks to windows
map.hbr | Map from reconstructed haplotype-blocks to windows
markers | Markers of the specified reconstructed haplotype-block
markers-method | Markers of the specified reconstructed haplotype-block
markers.hbr | Markers of the specified reconstructed haplotype-block
number_hbr | The number of reconstructed haplotype-block
number_hbr-method | The number of reconstructed haplotype-block
number_hbr.hbr | The number of reconstructed haplotype-block
plot-method | Method to visualize reconstructed haplotype-blocks
plot.hbr | Method to visualize reconstructed haplotype-blocks
plot_cluster_trajectories | Method to visualize the trajectories for all identified clusters in a window
plot_cluster_trajectories-method | Method to visualize the trajectories for all identified clusters in a window
plot_cluster_trajectories.hbr | Method to visualize the trajectories for all identified clusters in a window
plot_hbr-freq.hbr | Plots frequencies of a reconstructed haplotype-block along the chromosome
plot_hbr_freq | Plots frequencies of a reconstructed haplotype-block along the chromosome
plot_hbr_freq-method | Plots frequencies of a reconstructed haplotype-block along the chromosome
plot_marker_trajectories | Method to visualize the trajectories for all markers in a haplotype-block
plot_marker_trajectories-method | Method to visualize the trajectories for all markers in a haplotype-block
plot_marker_trajectories.hbr | Method to visualize the trajectories for all markers in a haplotype-block
reconstruct_hb | Reconstruction of haplotype-blocks
reconstruct_hb-method | Reconstruction of haplotype-blocks
reconstruct_hb.SNP_time_series | Reconstruction of haplotype-blocks
rev_map | Map from windows to reconstructed haplotype-blocks
rev_map-method | Map from windows to reconstructed haplotype-blocks
rev_map.hbr | Map from windows to reconstructed haplotype-blocks
show | Display of a hbr object
show-method | Display of a SNP_time_series object
show-method | Display of a hbr object
show.hbr | Display of a hbr object
show.SNP_time_series | Display of a SNP_time_series object
SNP_time_series | An S4 class storing time series data
SNP_time_series-class | An S4 class storing time series data
summary-method | Method to summarize information of reconstructed haplotype-blocks
summary.hbr | Method to summarize information of reconstructed haplotype-blocks
sync_to_frequencies | Data input from a sync file