Files in stephenslab/LDshrink
Implementation of Wen and Stephens 2010 LD shrinkage estimator

.Rbuildignore
.gitignore
DESCRIPTION
LDshrink.Rproj
NAMESPACE
R/LDshrink.R R/RcppExports.R R/block_utils.R R/catch-routine-registration.R R/gds_utils.R
R/libutils.R
README.md data-raw/download_map.R data-raw/gds_hap.R data-raw/panel_ld.R
data/CEU_map.rda
data/break_df.rda
data/map_parameters.rda
data/mapdat.rda
inst/HapmapII_GRCh37_RecombinationHotspots.tar.gz
inst/include/LDshrink.h
inst/include/LDshrink/LD.h
inst/include/LDshrink/mapdiff.hpp
inst/include/meta/meta.hpp
inst/include/meta/meta_fwd.hpp
inst/include/module.modulemap
inst/include/range/v3/action.hpp
inst/include/range/v3/action/action.hpp
inst/include/range/v3/action/concepts.hpp
inst/include/range/v3/action/drop.hpp
inst/include/range/v3/action/drop_while.hpp
inst/include/range/v3/action/erase.hpp
inst/include/range/v3/action/insert.hpp
inst/include/range/v3/action/join.hpp
inst/include/range/v3/action/push_back.hpp
inst/include/range/v3/action/push_front.hpp
inst/include/range/v3/action/remove_if.hpp
inst/include/range/v3/action/reverse.hpp
inst/include/range/v3/action/shuffle.hpp
inst/include/range/v3/action/slice.hpp
inst/include/range/v3/action/sort.hpp
inst/include/range/v3/action/split.hpp
inst/include/range/v3/action/stable_sort.hpp
inst/include/range/v3/action/stride.hpp
inst/include/range/v3/action/take.hpp
inst/include/range/v3/action/take_while.hpp
inst/include/range/v3/action/transform.hpp
inst/include/range/v3/action/unique.hpp
inst/include/range/v3/algorithm.hpp
inst/include/range/v3/algorithm/adjacent_find.hpp
inst/include/range/v3/algorithm/all_of.hpp
inst/include/range/v3/algorithm/any_of.hpp
inst/include/range/v3/algorithm/aux_/equal_range_n.hpp
inst/include/range/v3/algorithm/aux_/lower_bound_n.hpp
inst/include/range/v3/algorithm/aux_/merge_n.hpp
inst/include/range/v3/algorithm/aux_/merge_n_with_buffer.hpp
inst/include/range/v3/algorithm/aux_/partition_point_n.hpp
inst/include/range/v3/algorithm/aux_/sort_n_with_buffer.hpp
inst/include/range/v3/algorithm/aux_/upper_bound_n.hpp
inst/include/range/v3/algorithm/binary_search.hpp
inst/include/range/v3/algorithm/copy.hpp
inst/include/range/v3/algorithm/copy_backward.hpp
inst/include/range/v3/algorithm/copy_if.hpp
inst/include/range/v3/algorithm/copy_n.hpp
inst/include/range/v3/algorithm/count.hpp
inst/include/range/v3/algorithm/count_if.hpp
inst/include/range/v3/algorithm/equal.hpp
inst/include/range/v3/algorithm/equal_range.hpp
inst/include/range/v3/algorithm/fill.hpp
inst/include/range/v3/algorithm/fill_n.hpp
inst/include/range/v3/algorithm/find.hpp
inst/include/range/v3/algorithm/find_end.hpp
inst/include/range/v3/algorithm/find_first_of.hpp
inst/include/range/v3/algorithm/find_if.hpp
inst/include/range/v3/algorithm/find_if_not.hpp
inst/include/range/v3/algorithm/for_each.hpp
inst/include/range/v3/algorithm/for_each_n.hpp
inst/include/range/v3/algorithm/generate.hpp
inst/include/range/v3/algorithm/generate_n.hpp
inst/include/range/v3/algorithm/heap_algorithm.hpp
inst/include/range/v3/algorithm/inplace_merge.hpp
inst/include/range/v3/algorithm/is_partitioned.hpp
inst/include/range/v3/algorithm/is_sorted.hpp
inst/include/range/v3/algorithm/is_sorted_until.hpp
inst/include/range/v3/algorithm/lexicographical_compare.hpp
inst/include/range/v3/algorithm/lower_bound.hpp
inst/include/range/v3/algorithm/max.hpp
inst/include/range/v3/algorithm/max_element.hpp
inst/include/range/v3/algorithm/merge.hpp
inst/include/range/v3/algorithm/min.hpp
inst/include/range/v3/algorithm/min_element.hpp
inst/include/range/v3/algorithm/minmax.hpp
inst/include/range/v3/algorithm/minmax_element.hpp
inst/include/range/v3/algorithm/mismatch.hpp
inst/include/range/v3/algorithm/move.hpp
inst/include/range/v3/algorithm/move_backward.hpp
inst/include/range/v3/algorithm/none_of.hpp
inst/include/range/v3/algorithm/nth_element.hpp
inst/include/range/v3/algorithm/partial_sort.hpp
inst/include/range/v3/algorithm/partial_sort_copy.hpp
inst/include/range/v3/algorithm/partition.hpp
inst/include/range/v3/algorithm/partition_copy.hpp
inst/include/range/v3/algorithm/partition_point.hpp
inst/include/range/v3/algorithm/permutation.hpp
inst/include/range/v3/algorithm/remove.hpp
inst/include/range/v3/algorithm/remove_copy.hpp
inst/include/range/v3/algorithm/remove_copy_if.hpp
inst/include/range/v3/algorithm/remove_if.hpp
inst/include/range/v3/algorithm/replace.hpp
inst/include/range/v3/algorithm/replace_copy.hpp
inst/include/range/v3/algorithm/replace_copy_if.hpp
inst/include/range/v3/algorithm/replace_if.hpp
inst/include/range/v3/algorithm/reverse.hpp
inst/include/range/v3/algorithm/reverse_copy.hpp
inst/include/range/v3/algorithm/rotate.hpp
inst/include/range/v3/algorithm/rotate_copy.hpp
inst/include/range/v3/algorithm/sample.hpp
inst/include/range/v3/algorithm/search.hpp
inst/include/range/v3/algorithm/search_n.hpp
inst/include/range/v3/algorithm/set_algorithm.hpp
inst/include/range/v3/algorithm/shuffle.hpp
inst/include/range/v3/algorithm/sort.hpp
inst/include/range/v3/algorithm/stable_partition.hpp
inst/include/range/v3/algorithm/stable_sort.hpp
inst/include/range/v3/algorithm/swap_ranges.hpp
inst/include/range/v3/algorithm/tagspec.hpp
inst/include/range/v3/algorithm/transform.hpp
inst/include/range/v3/algorithm/unique.hpp
inst/include/range/v3/algorithm/unique_copy.hpp
inst/include/range/v3/algorithm/upper_bound.hpp
inst/include/range/v3/all.hpp
inst/include/range/v3/at.hpp
inst/include/range/v3/back.hpp
inst/include/range/v3/begin_end.hpp
inst/include/range/v3/core.hpp
inst/include/range/v3/data.hpp
inst/include/range/v3/detail/config.hpp
inst/include/range/v3/detail/satisfy_boost_range.hpp
inst/include/range/v3/detail/variant.hpp
inst/include/range/v3/distance.hpp
inst/include/range/v3/empty.hpp
inst/include/range/v3/experimental/utility/generator.hpp
inst/include/range/v3/experimental/view/shared.hpp
inst/include/range/v3/front.hpp
inst/include/range/v3/getlines.hpp
inst/include/range/v3/index.hpp
inst/include/range/v3/istream_range.hpp
inst/include/range/v3/iterator_range.hpp
inst/include/range/v3/numeric.hpp
inst/include/range/v3/numeric/accumulate.hpp
inst/include/range/v3/numeric/adjacent_difference.hpp
inst/include/range/v3/numeric/inner_product.hpp
inst/include/range/v3/numeric/iota.hpp
inst/include/range/v3/numeric/partial_sum.hpp
inst/include/range/v3/range_access.hpp
inst/include/range/v3/range_concepts.hpp
inst/include/range/v3/range_for.hpp
inst/include/range/v3/range_fwd.hpp
inst/include/range/v3/range_traits.hpp
inst/include/range/v3/size.hpp
inst/include/range/v3/span.hpp
inst/include/range/v3/to_container.hpp
inst/include/range/v3/utility/any.hpp
inst/include/range/v3/utility/associated_types.hpp
inst/include/range/v3/utility/basic_iterator.hpp
inst/include/range/v3/utility/box.hpp
inst/include/range/v3/utility/common_iterator.hpp
inst/include/range/v3/utility/common_tuple.hpp
inst/include/range/v3/utility/common_type.hpp
inst/include/range/v3/utility/compressed_pair.hpp
inst/include/range/v3/utility/concepts.hpp
inst/include/range/v3/utility/copy.hpp
inst/include/range/v3/utility/counted_iterator.hpp
inst/include/range/v3/utility/dangling.hpp
inst/include/range/v3/utility/functional.hpp
inst/include/range/v3/utility/get.hpp
inst/include/range/v3/utility/infinity.hpp
inst/include/range/v3/utility/invoke.hpp
inst/include/range/v3/utility/iterator.hpp
inst/include/range/v3/utility/iterator_concepts.hpp
inst/include/range/v3/utility/iterator_traits.hpp
inst/include/range/v3/utility/memory.hpp
inst/include/range/v3/utility/move.hpp
inst/include/range/v3/utility/nullptr_v.hpp
inst/include/range/v3/utility/optional.hpp
inst/include/range/v3/utility/polymorphic_cast.hpp
inst/include/range/v3/utility/random.hpp
inst/include/range/v3/utility/safe_int.hpp
inst/include/range/v3/utility/scope_exit.hpp
inst/include/range/v3/utility/semiregular.hpp
inst/include/range/v3/utility/static_const.hpp
inst/include/range/v3/utility/swap.hpp
inst/include/range/v3/utility/tagged_pair.hpp
inst/include/range/v3/utility/tagged_tuple.hpp
inst/include/range/v3/utility/tuple_algorithm.hpp
inst/include/range/v3/utility/unreachable.hpp
inst/include/range/v3/utility/variant.hpp
inst/include/range/v3/version.hpp
inst/include/range/v3/view.hpp
inst/include/range/v3/view/adjacent_filter.hpp
inst/include/range/v3/view/adjacent_remove_if.hpp
inst/include/range/v3/view/all.hpp
inst/include/range/v3/view/any_view.hpp
inst/include/range/v3/view/bounded.hpp
inst/include/range/v3/view/c_str.hpp
inst/include/range/v3/view/cartesian_product.hpp
inst/include/range/v3/view/chunk.hpp
inst/include/range/v3/view/concat.hpp
inst/include/range/v3/view/const.hpp
inst/include/range/v3/view/counted.hpp
inst/include/range/v3/view/cycle.hpp
inst/include/range/v3/view/delimit.hpp
inst/include/range/v3/view/drop.hpp
inst/include/range/v3/view/drop_exactly.hpp
inst/include/range/v3/view/drop_while.hpp
inst/include/range/v3/view/empty.hpp
inst/include/range/v3/view/filter.hpp
inst/include/range/v3/view/for_each.hpp
inst/include/range/v3/view/generate.hpp
inst/include/range/v3/view/generate_n.hpp
inst/include/range/v3/view/group_by.hpp
inst/include/range/v3/view/indices.hpp
inst/include/range/v3/view/indirect.hpp
inst/include/range/v3/view/intersperse.hpp
inst/include/range/v3/view/iota.hpp
inst/include/range/v3/view/join.hpp
inst/include/range/v3/view/linear_distribute.hpp
inst/include/range/v3/view/map.hpp
inst/include/range/v3/view/move.hpp
inst/include/range/v3/view/partial_sum.hpp
inst/include/range/v3/view/remove_if.hpp
inst/include/range/v3/view/repeat.hpp
inst/include/range/v3/view/repeat_n.hpp
inst/include/range/v3/view/replace.hpp
inst/include/range/v3/view/replace_if.hpp
inst/include/range/v3/view/reverse.hpp
inst/include/range/v3/view/sample.hpp
inst/include/range/v3/view/set_algorithm.hpp
inst/include/range/v3/view/single.hpp
inst/include/range/v3/view/slice.hpp
inst/include/range/v3/view/sliding.hpp
inst/include/range/v3/view/split.hpp
inst/include/range/v3/view/stride.hpp
inst/include/range/v3/view/tail.hpp
inst/include/range/v3/view/take.hpp
inst/include/range/v3/view/take_exactly.hpp
inst/include/range/v3/view/take_while.hpp
inst/include/range/v3/view/tokenize.hpp
inst/include/range/v3/view/transform.hpp
inst/include/range/v3/view/unbounded.hpp
inst/include/range/v3/view/unique.hpp
inst/include/range/v3/view/view.hpp
inst/include/range/v3/view/zip.hpp
inst/include/range/v3/view/zip_with.hpp
inst/include/range/v3/view_adaptor.hpp
inst/include/range/v3/view_facade.hpp
inst/include/range/v3/view_interface.hpp
inst/ldetect_files/P00_00_partition_chromosome.py
inst/ldetect_files/P00_01_calc_covariance.py
inst/ldetect_files/P01_matrix_to_vector_pipeline.py
inst/ldetect_files/P02_minima_pipeline.py
inst/ldetect_files/P03_extract_bpoints.py
inst/ldetect_files/partition_chromosome.py
inst/m_files/compute_shrinkage.m
inst/m_files/compute_shrinkage.m~
inst/m_files/corrcov.m
inst/m_files/corrcov.m~
inst/m_files/get_corr.m
inst/m_files/get_corr_d.m
inst/m_files/get_corr_d.m~
inst/m_files/shrink_cov.m
inst/m_files/shrink_cov.m~
inst/m_files/shrink_m.m
inst/m_files/shrink_m.m~
inst/m_files/wrap_corr.m
inst/m_files/wrap_corr.m~
inst/test_gdsf/fourier_ls-all.bed
inst/test_gdsf/map_sub_19.txt.gz
inst/test_gdsf/sub_19.gds
inst/test_gdsf/sub_19.impute.hap
inst/test_gdsf/sub_19.impute.hap.indv
inst/test_gdsf/sub_19.impute.legend
inst/test_gdsf/sub_19.log
inst/test_gdsf/sub_19.recode.vcf
inst/test_gdsf/sub_snpid.txt
man/assign_map.Rd man/assign_snp_block.Rd man/calc_theta.Rd man/ld2df.Rd
src/LD.cpp
src/LD_p.cpp
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/SNPcoord.cpp
src/test-example.cpp
src/test-runner.cpp
tests/testthat.R tests/testthat/test-cpp.R tests/testthat/test_LD.R tests/testthat/test_util.R
stephenslab/LDshrink documentation built on Aug. 22, 2018, 5:25 p.m.