R-package: Calculation of haplotype blocks and libraries
This is the github repository for your R-package HaploBlocker. A paper on HaploBlocker has been published in Genetics (https://www.genetics.org/content/212/4/1045)
The newest release 1.6.0 is mostly adding an optional modus to identify non-overlapping blocks. Outputs on defaults should be the same. The newest version of HaploBlocker is using RandomFieldsUtils 0.6.6 (This is more than what is available on CRAN!). 1.5.X is using 0.5.9, 1.4.X and below is using RandomFieldsUtils 0.5.3.
For further questions (torsten.pook@uni-goettingen.de)
For explanation on the usage we refer to our user manual. The wiki is currently not equivilant (https://github.com/tpook92/HaploBlocker/wiki) - its just a couple of figure and not top priority as the user manual (Guidelines_to_HaploBlocker) should do.
Fixed typo in parallel computing
Improved data import from vcf/ped-file
RandomFieldsUtils update (0.6.6)
Hotfixes in utility/plot functions
Added blocklist_subset to only consider a subset of haplotypes in the haplotype library
Updates for the use in graph-genomes (extended doku will follow)
Added the option to identify non-overlapping haplotype blocks (overlap_remove = TRUE in block_calculation() )
Minor improvments to block_windowdataset()
Hotfixes in plot_block, block_calculation when providing base-pair info
HaploBlocker has been officially been published in Genetics (https://www.genetics.org/content/early/2019/05/31/genetics.119.302283)
A frozen version of the current package has been added in "Genetics_submission_version"
Min_majorblock is now automatically reduced in case the current parametrization would lead to a empty blocklist // haplotype library
Removed typo in plot_block
Support usage of vcf and pedmap files as input for genetic datasets
Creating of a window dataset (block_windowdataset). Block structure more similar to traditional haplotype block methods (set start/end points etc.)
Improvement to documentation (Guidelines_to_HaploBlocker)
Hotfix in block_dataset_construction
New features: selection signature detection (bEHH, iHH)
Improved computing time: (parallel computing, skipping unnecessary steps for large scale datasets)
Minor updates to RandomFieldsUtils: 0.4.0+ now required (available at CRAN)
Initial release