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Guide
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A
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B
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C
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D
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E
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F
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G
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I
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J
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L
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M
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N
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O
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P
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R
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S
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T
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V
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W
A
add() (snipar.gtarray.gtarray method)
add_control() (in module snipar.imputation.preprocess_data)
alpha_mle() (snipar.lmm.model method)
am_indices() (in module snipar.simulate)
B
bayes_shrink() (snipar.errors.g_error method)
C
compute() (in module snipar.pgs)
(snipar.pgs.pgs method)
compute_aics() (in module snipar.imputation.preprocess_data)
compute_batch_boundaries() (in module snipar.gwas)
compute_corr() (in module snipar.correlate)
compute_freqs() (snipar.gtarray.gtarray method)
compute_genetic_component() (in module snipar.simulate)
compute_info() (snipar.gtarray.gtarray method)
compute_ld_scores() (in module snipar.ld)
(snipar.correlate.sumstats method)
compute_phenotype() (in module snipar.simulate)
compute_phenotype_indirect() (in module snipar.simulate)
compute_phenotype_vert() (in module snipar.simulate)
compute_ses() (in module snipar.gwas)
concatenate() (snipar.correlate.sumstats method)
convert_str_array() (in module snipar.utilities)
cor_direct_avg_NTC() (snipar.correlate.sumstats method)
cor_direct_pop() (snipar.correlate.sumstats method)
count_ME() (in module snipar.errors)
create_graph_from_pedigree() (in module snipar.tests.test_pedigree_creation)
create_pedigree() (in module snipar.imputation.preprocess_data)
(in module snipar.pedigree)
D
decode_map_from_pos() (in module snipar.map)
diagonalise() (snipar.gtarray.gtarray method)
E
encode_str_array() (in module snipar.utilities)
estimate_f() (in module snipar.imputation.preprocess_data)
estimate_genotyping_error_rate() (in module snipar.errors)
F
fill_NAs() (snipar.gtarray.gtarray method)
filter() (snipar.correlate.sumstats method)
(snipar.gtarray.gtarray method)
filter_corrs() (snipar.correlate.sumstats method)
filter_ids() (snipar.gtarray.gtarray method)
filter_info() (snipar.gtarray.gtarray method)
filter_maf() (snipar.correlate.sumstats method)
(snipar.gtarray.gtarray method)
filter_missingness() (snipar.gtarray.gtarray method)
filter_NAs() (snipar.correlate.sumstats method)
find_individuals_with_sibs() (in module snipar.pedigree)
find_par_gts() (in module snipar.preprocess)
find_segments() (in module snipar.ibd)
fit_model() (in module snipar.lmm)
fit_models() (in module snipar.gwas)
G
g_error (class in snipar.errors)
get_fam_means() (in module snipar.preprocess)
get_gts_matrix() (in module snipar.read)
get_gts_matrix_given_ped() (in module snipar.read.bed)
(in module snipar.read.bgen)
get_indices_given_ped() (in module snipar.preprocess)
get_map_positions() (in module snipar.map)
get_sibpairs_from_king() (in module snipar.pedigree)
get_sibpairs_from_ped() (in module snipar.pedigree)
get_snps() (in module snipar.read.bed)
(in module snipar.read.bgen)
gtarray (class in snipar.gtarray)
I
imputation_test() (in module snipar.tests.test_imputation)
(in module snipar.tests.test_manhattan)
impute() (in module snipar.imputation.impute_from_sibs)
impute_all_fams() (in module snipar.simulate)
impute_all_fams_phased() (in module snipar.simulate)
impute_from_sibs() (in module snipar.simulate)
impute_from_sibs_phased() (in module snipar.simulate)
infer_ibd() (in module snipar.ibd)
infer_ibd_chr() (in module snipar.ibd)
J
jacknife() (in module snipar.correlate)
jacknife_est() (in module snipar.correlate)
L
ldscores_from_bed() (in module snipar.ld)
lik_and_grad() (in module snipar.lmm)
likelihood_and_gradient() (snipar.lmm.model method)
load_example_data() (in module snipar.example.snipar_example_data)
log (snipar.tests.utils.SniparTest attribute)
M
main() (in module snipar.example.simulate_phenotype)
(in module snipar.scripts.correlate)
(in module snipar.scripts.gwas)
(in module snipar.scripts.ibd)
(in module snipar.scripts.impute)
(in module snipar.scripts.pgs)
(in module snipar.scripts.simulate)
make_dynamic() (in module snipar.ibd)
make_gts_matrix() (in module snipar.preprocess)
make_id_dict() (in module snipar.utilities)
map_from_bed() (in module snipar.map)
match_observed_and_imputed_snps() (in module snipar.read.bed)
(in module snipar.read.bgen)
match_phenotype() (in module snipar.read.phenotype)
mean_normalise() (snipar.gtarray.gtarray method)
meiosis() (in module snipar.simulate)
mendelian_errors() (in module snipar.errors)
model (class in snipar.lmm)
module
snipar
snipar.config
snipar.correlate
snipar.errors
snipar.example
snipar.example.simulate_phenotype
snipar.example.snipar_example_data
snipar.gtarray
snipar.gwas
snipar.ibd
snipar.imputation
snipar.imputation.impute_from_sibs
snipar.imputation.preprocess_data
snipar.ld
snipar.lmm
snipar.map
snipar.pedigree
snipar.pgs
snipar.preprocess
snipar.read
snipar.read.bed
snipar.read.bgen
snipar.read.phenotype
snipar.scripts
snipar.scripts.correlate
snipar.scripts.gwas
snipar.scripts.ibd
snipar.scripts.impute
snipar.scripts.pgs
snipar.scripts.simulate
snipar.simulate
snipar.tests
snipar.tests.test_example
snipar.tests.test_imputation
snipar.tests.test_impute
snipar.tests.test_impute_from_sibs
snipar.tests.test_manhattan
snipar.tests.test_pedigree_creation
snipar.tests.test_sibreg
snipar.tests.utils
snipar.utilities
N
node_match() (in module snipar.tests.test_pedigree_creation)
NumRangeAction (class in snipar.utilities)
O
optimize_model() (snipar.lmm.model method)
outarray_effect() (in module snipar.gwas)
outfile_name() (in module snipar.utilities)
P
p_ibd_0() (in module snipar.ibd)
p_ibd_1() (in module snipar.ibd)
p_ibd_2() (in module snipar.ibd)
p_obs_given_IBD() (in module snipar.ibd)
p_value_threshold (snipar.tests.utils.SniparTest attribute)
parse_filelist() (in module snipar.utilities)
parse_obsfiles() (in module snipar.utilities)
parseNumRange() (in module snipar.utilities)
Person (class in snipar.imputation.preprocess_data)
(class in snipar.pedigree)
pgs (class in snipar.pgs)
pos_to_cM() (in module snipar.map)
predict() (snipar.lmm.model method)
prepare_data() (in module snipar.imputation.preprocess_data)
prepare_gts() (in module snipar.imputation.preprocess_data)
preprocess_king() (in module snipar.imputation.preprocess_data)
process_batch() (in module snipar.gwas)
process_chromosome() (in module snipar.gwas)
produce_next_gen() (in module snipar.simulate)
R
r2_est() (in module snipar.ld)
random_design() (in module snipar.tests.test_sibreg)
random_mating_indices() (in module snipar.simulate)
read_covariates() (in module snipar.read.phenotype)
read_phenotype() (in module snipar.read.phenotype)
read_PO_pairs_from_bed() (in module snipar.read.bed)
read_PO_pairs_from_bgen() (in module snipar.read.bgen)
read_sibs_from_bed() (in module snipar.read.bed)
read_sibs_from_bgen() (in module snipar.read.bgen)
read_sumstats_file() (in module snipar.correlate)
read_sumstats_files() (in module snipar.correlate)
recurcive_append() (in module snipar.imputation.preprocess_data)
run_imputation() (in module snipar.scripts.impute)
S
safe_alpha_mle() (in module snipar.tests.test_sibreg)
safe_likelihood() (in module snipar.tests.test_sibreg)
scale() (snipar.gtarray.gtarray method)
scores_from_ldsc() (snipar.correlate.sumstats method)
segment (class in snipar.ibd)
set_alpha() (snipar.lmm.model method)
setUp() (snipar.tests.utils.SniparTest method)
setUpClass() (snipar.tests.utils.SniparTest class method)
sigma_inv_root() (snipar.lmm.model method)
Sigma_make() (in module snipar.tests.test_sibreg)
simulate() (in module snipar.lmm)
simulate_recombinations() (in module snipar.simulate)
smooth_ibd() (in module snipar.ibd)
smooth_segments() (in module snipar.ibd)
snipar
module
snipar.config
module
snipar.correlate
module
snipar.errors
module
snipar.example
module
snipar.example.simulate_phenotype
module
snipar.example.snipar_example_data
module
snipar.gtarray
module
snipar.gwas
module
snipar.ibd
module
snipar.imputation
module
snipar.imputation.impute_from_sibs
module
snipar.imputation.preprocess_data
module
snipar.ld
module
snipar.lmm
module
snipar.map
module
snipar.pedigree
module
snipar.pgs
module
snipar.preprocess
module
snipar.read
module
snipar.read.bed
module
snipar.read.bgen
module
snipar.read.phenotype
module
snipar.scripts
module
snipar.scripts.correlate
module
snipar.scripts.gwas
module
snipar.scripts.ibd
module
snipar.scripts.impute
module
snipar.scripts.pgs
module
snipar.scripts.simulate
module
snipar.simulate
module
snipar.tests
module
snipar.tests.test_example
module
snipar.tests.test_imputation
module
snipar.tests.test_impute
module
snipar.tests.test_impute_from_sibs
module
snipar.tests.test_manhattan
module
snipar.tests.test_pedigree_creation
module
snipar.tests.test_sibreg
module
snipar.tests.utils
module
snipar.utilities
module
SniparTest (class in snipar.tests.utils)
subsample_snp (snipar.tests.utils.SniparTest attribute)
sumstats (class in snipar.correlate)
T
tearDown() (snipar.tests.utils.SniparTest method)
tearDownClass() (snipar.tests.utils.SniparTest class method)
test_add_control() (snipar.tests.test_pedigree_creation.TestPedigree method)
test_alpha_mle() (snipar.tests.test_sibreg.test_regrnd_functions method)
test_create_pedigree() (snipar.tests.test_pedigree_creation.TestPedigree method)
test_dict_to_cmap() (snipar.tests.test_impute_from_sibs.TestSibImpute method)
test_example() (snipar.tests.test_example.TestExample method)
test_get_IBD() (snipar.tests.test_impute_from_sibs.TestSibImpute method)
test_get_IBD_type() (snipar.tests.test_impute_from_sibs.TestSibImpute method)
test_grad_sigma2() (snipar.tests.test_sibreg.test_regrnd_functions method)
test_grad_tau() (snipar.tests.test_sibreg.test_regrnd_functions method)
test_impute_snp_from_offsprings_unphased() (snipar.tests.test_impute_from_sibs.TestSibImpute method)
test_impute_snp_from_parent_offsprings_unphased() (snipar.tests.test_impute_from_sibs.TestSibImpute method)
test_impute_with_phased_pedigree_chunks_control() (snipar.tests.test_impute.TestImpute method)
test_impute_with_phased_pedigree_control() (snipar.tests.test_impute.TestImpute method)
test_impute_with_unphased_king() (snipar.tests.test_impute.TestImpute method)
test_impute_with_unphased_king_control() (snipar.tests.test_impute.TestImpute method)
test_impute_with_unphased_king_control_legacy_ibd() (snipar.tests.test_impute.TestImpute method)
test_impute_with_unphased_king_control_legacy_tilda_ibd() (snipar.tests.test_impute.TestImpute method)
test_impute_with_unphased_king_control_pca() (snipar.tests.test_impute.TestImpute method)
test_impute_with_unphased_pedigree() (snipar.tests.test_impute.TestImpute method)
test_impute_with_unphased_pedigree_chunks_control() (snipar.tests.test_impute.TestImpute method)
test_impute_with_unphased_pedigree_control() (snipar.tests.test_impute.TestImpute method)
test_impute_with_unphased_pedigree_control_backup() (snipar.tests.test_impute.TestImpute method)
test_impute_with_unphased_pedigree_control_legacy_ibd() (snipar.tests.test_impute.TestImpute method)
test_impute_with_unphased_pedigree_control_multiprocess() (snipar.tests.test_impute.TestImpute method)
test_impute_with_unphased_pedigree_control_nothread() (snipar.tests.test_impute.TestImpute method)
test_impute_with_unphased_pedigree_control_notilda() (snipar.tests.test_impute.TestImpute method)
test_impute_with_unphased_pedigree_wild_ibd_control() (snipar.tests.test_impute.TestImpute method)
test_likelihood() (snipar.tests.test_sibreg.test_regrnd_functions method)
test_regrnd_functions (class in snipar.tests.test_sibreg)
TestExample (class in snipar.tests.test_example)
TestImpute (class in snipar.tests.test_impute)
TestPedigree (class in snipar.tests.test_pedigree_creation)
TestSibImpute (class in snipar.tests.test_impute_from_sibs)
to_text() (snipar.ibd.segment method)
transform_phenotype() (in module snipar.gwas)
transition_matrix() (in module snipar.ibd)
V
viterbi() (in module snipar.ibd)
W
write() (in module snipar.pgs)
write_output() (in module snipar.gwas)
write_segs() (in module snipar.ibd)
write_segs_from_matrix() (in module snipar.ibd)
write_txt_output() (in module snipar.gwas)
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