Reconstruction of Haplotype-Blocks from Time Series Data

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Documentation for package ‘haploReconstruct’ version 0.1.2

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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