haploReconstruct: Reconstruction of Haplotype-Blocks from Time Series Data

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Reconstruction of founder haplotype blocks from time series data.

Author
Susanne U. Franssen, Nicholas H. Barton, Christian Schloetterer
Date of publication
2016-10-10 18:18:49
Maintainer
Susanne U. Franssen <susefranssen@googlemail.com>
License
GPL-3
Version
0.1.2

View on CRAN

Man pages

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

Files in this package

haploReconstruct
haploReconstruct/NAMESPACE
haploReconstruct/data
haploReconstruct/data/datalist
haploReconstruct/data/ex_dat.rda
haploReconstruct/R
haploReconstruct/R/AllGenerics.R
haploReconstruct/R/methods-hbr.R
haploReconstruct/R/Data.Classes.R
haploReconstruct/R/haploReconstruct.R
haploReconstruct/R/ex_dat.r
haploReconstruct/R/functions-hbr.R
haploReconstruct/R/functions-read-sync.R
haploReconstruct/R/methods-SNP_time_series.R
haploReconstruct/R/functions-SNP_time_series.R
haploReconstruct/MD5
haploReconstruct/DESCRIPTION
haploReconstruct/man
haploReconstruct/man/show-hbr-method.Rd
haploReconstruct/man/plot_marker_trajectories-hbr-method.Rd
haploReconstruct/man/plot_hbr_freq-hbr-method.Rd
haploReconstruct/man/markers-hbr-method.Rd
haploReconstruct/man/number_hbr-hbr-method.Rd
haploReconstruct/man/inspect_window_PCA-hbr-method.Rd
haploReconstruct/man/ex_dat.Rd
haploReconstruct/man/reconstruct_hb-SNP_time_series-method.Rd
haploReconstruct/man/map-hbr-method.Rd
haploReconstruct/man/initialize_SNP_time_series.Rd
haploReconstruct/man/inspect_window-hbr-method.Rd
haploReconstruct/man/inspect_window_dbScan-hbr-method.Rd
haploReconstruct/man/plot_cluster_trajectories-hbr-method.Rd
haploReconstruct/man/sync_to_frequencies.Rd
haploReconstruct/man/hbr-class.Rd
haploReconstruct/man/inspect_window_avLink-hbr-method.Rd
haploReconstruct/man/SNP_time_series-class.Rd
haploReconstruct/man/plot-hbr-method.Rd
haploReconstruct/man/rev_map-hbr-method.Rd
haploReconstruct/man/show-SNP_time_series-method.Rd
haploReconstruct/man/summary-hbr-method.Rd