Index

Symbols

--allele happler-transform command line option --chunk-size happler-run command line option happler-transform command line option --discard-missing happler-run command line option happler-transform command line option --discard-multiallelic happler-run command line option happler-transform command line option --hap-id happler-transform command line option --hap-maf happler-run command line option --ld-prune-thresh happler-run command line option --maf happler-run command line option happler-transform command line option --max-iterations happler-run command line option --max-signals happler-run command line option --out-thresh happler-run command line option --output happler-run command line option happler-transform command line option --pheno happler-run command line option --pheno-name happler-run command line option --region happler-run command line option happler-transform command line option

--remove-SNPs happler-run command line option --sample happler-run command line option happler-transform command line option --samples-file happler-run command line option happler-transform command line option --show-tree happler-run command line option --var-id happler-transform command line option --verbosity happler-run command line option happler-transform command line option --version happler command line option -a happler-transform command line option -c happler-run command line option happler-transform command line option -i happler-transform command line option -o happler-run command line option happler-transform command line option -S happler-run command line option happler-transform command line option -s happler-run command line option happler-transform command line option -v happler-run command line option happler-transform command line option

A

add_node() (happler.tree.tree.Tree method) append() (happler.tree.haplotypes.Haplotype method) AssocResults (class in happler.tree.assoc_test) AssocTest (class in happler.tree.assoc_test)

AssocTestSimple (class in happler.tree.assoc_test) AssocTestSimpleCovariates (class in happler.tree.assoc_test) AssocTestSimpleFastBIC (class in happler.tree.assoc_test) AssocTestSimpleSM (class in happler.tree.assoc_test) AssocTestSimpleSMTScore (class in happler.tree.assoc_test)

B

beta (happler.tree.assoc_test.NodeResults attribute) (happler.tree.haplotypes.HapplerHaplotype attribute)

bic (happler.tree.assoc_test.NodeResultsBIC attribute) (happler.tree.assoc_test.NodeResultsExtra attribute) bic() (happler.tree.assoc_test.AssocTestSimple method)

D

data (happler.tree.assoc_test.AssocResults attribute) (happler.tree.haplotypes.Haplotype attribute)

dot() (happler.tree.tree.Tree method)

F

from_haptools_haplotype() (happler.tree.haplotypes.Haplotype class method) from_node() (happler.tree.haplotypes.Haplotype class method) from_np() (happler.tree.assoc_test.NodeResults class method) (happler.tree.assoc_test.NodeResultsBIC class method) (happler.tree.variant.Variant class method)

from_tree() (happler.tree.haplotypes.Haplotypes class method)

G

GENOTYPES happler-run command line option happler-transform command line option

H

Haplotype (class in happler.tree.haplotypes) HAPLOTYPES happler-transform command line option Haplotypes (class in happler.tree.haplotypes) haplotypes() (happler.tree.tree.Tree method) happler command line option --version happler-run command line option --chunk-size --discard-missing --discard-multiallelic --hap-maf --ld-prune-thresh --maf --max-iterations --max-signals --out-thresh --output --pheno --pheno-name --region --remove-SNPs --sample --samples-file --show-tree --verbosity -c -o -s -S -v GENOTYPES PHENOTYPES

happler-transform command line option --allele --chunk-size --discard-missing --discard-multiallelic --hap-id --maf --output --region --sample --samples-file --var-id --verbosity -a -c -i -o -s -S -v GENOTYPES HAPLOTYPES happler.tree.assoc_test module happler.tree.haplotypes module happler.tree.tree module happler.tree.tree_builder module happler.tree.variant module HapplerHaplotype (class in happler.tree.haplotypes) HapplerVariant (class in happler.tree.haplotypes)

I

id (happler.tree.variant.Variant attribute)

ID (happler.tree.variant.Variant property) idx (happler.tree.variant.Variant attribute)

L

leaves() (happler.tree.tree.Tree method)

M

module happler.tree.assoc_test happler.tree.haplotypes happler.tree.tree happler.tree.tree_builder happler.tree.variant

N

node_indices (happler.tree.haplotypes.Haplotype property) NodeResults (class in happler.tree.assoc_test) NodeResultsBIC (class in happler.tree.assoc_test) NodeResultsExtra (class in happler.tree.assoc_test)

NodeResultsExtraTScore (class in happler.tree.assoc_test) NodeResultsTScore (class in happler.tree.assoc_test) nodes (happler.tree.haplotypes.Haplotype attribute) num_nodes (happler.tree.tree.Tree property) num_variants (happler.tree.tree.Tree property)

P

perform_test() (happler.tree.assoc_test.AssocTestSimple method) (happler.tree.assoc_test.AssocTestSimpleFastBIC method) (happler.tree.assoc_test.AssocTestSimpleSM method) (happler.tree.assoc_test.AssocTestSimpleSMTScore method) PHENOTYPES happler-run command line option

pos (happler.tree.variant.Variant attribute) POS (happler.tree.variant.Variant property) prune_tree() (happler.tree.tree_builder.TreeBuilder method) pval (happler.tree.assoc_test.NodeResults attribute) (happler.tree.haplotypes.HapplerHaplotype attribute) pval_as_decimal() (happler.tree.assoc_test.AssocTest static method)

R

remove_leaf_node() (happler.tree.tree.Tree method) run() (happler.tree.assoc_test.AssocTest method) (happler.tree.assoc_test.AssocTestSimple method) (happler.tree.assoc_test.AssocTestSimpleFastBIC method) (happler.tree.assoc_test.AssocTestSimpleSMTScore method) (happler.tree.tree_builder.TreeBuilder method)

S

score (happler.tree.haplotypes.HapplerVariant attribute) siblings() (happler.tree.tree.Tree method)

standardize() (happler.tree.assoc_test.AssocTest method) stderr (happler.tree.assoc_test.NodeResults attribute)

T

transform() (happler.tree.haplotypes.Haplotype method) transform_and_sum() (happler.tree.haplotypes.Haplotype method) Tree (class in happler.tree.tree)

TreeBuilder (class in happler.tree.tree_builder) tscore (happler.tree.assoc_test.NodeResultsExtraTScore attribute) (happler.tree.assoc_test.NodeResultsTScore attribute)

V

Variant (class in happler.tree.variant)

VariantType (class in happler.tree.variant)