Contents:
Guide
Tutorial
Input files
Output files
Command Line Scripts
Simulation Exercise
snipar
Index
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Index
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
J
|
K
|
L
|
M
|
N
|
O
|
P
|
R
|
S
|
T
|
V
|
W
A
add() (snipar.gtarray.gtarray method)
(snipar.pgs.pgarray method)
add_control() (in module snipar.imputation.preprocess_data)
ai_reml() (snipar.slmm.LinearMixedModel method)
alpha_from_alpha() (in module snipar.pgs_am)
alpha_from_beta() (in module snipar.pgs_am)
alpha_mle() (snipar.lmm.model method)
am_adj() (snipar.pgs.pgarray method)
am_adj_2gen() (in module snipar.pgs)
am_adj_2gen_calc() (in module snipar.pgs)
am_indices() (in module snipar.simulate)
B
bayes_shrink() (snipar.errors.g_error method)
build_grm_arr() (in module snipar.slmm)
build_ibdrel_arr() (in module snipar.slmm)
build_sib_arr() (in module snipar.slmm)
C
cached_property_depends_on() (in module snipar.slmm)
check_se_calc() (in module snipar.pgs_am)
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_grandpar() (snipar.pgs.pgarray method)
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)
compute_vcomps() (in module snipar.simulate)
concatenate() (snipar.correlate.sumstats method)
convert_str_array() (in module snipar.utilities)
coord2linear() (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_ped_output() (in module snipar.simulate)
create_pedigree() (in module snipar.pedigree)
D
decode_map_from_pos() (in module snipar.map)
delta_method() (in module snipar.pgs_am)
dense_reml_loglik() (snipar.slmm.LinearMixedModel method)
diagonalise() (snipar.gtarray.gtarray method)
E
encode_str_array() (in module snipar.utilities)
estimate_cov() (in module snipar.correlate)
estimate_cov_weights() (in module snipar.correlate)
estimate_f() (in module snipar.imputation.preprocess_data)
estimate_genotyping_error_rate() (in module snipar.errors)
estimate_h2eq() (in module snipar.pgs_am)
estimate_k() (in module snipar.pgs_am)
estimate_r() (in module snipar.pgs_am)
(snipar.pgs.pgarray method)
estimate_rho() (in module snipar.pgs_am)
estimate_var() (in module snipar.correlate)
estimate_weights() (in module snipar.correlate)
F
fill_NAs() (snipar.gtarray.gtarray method)
filter() (snipar.correlate.sumstats method)
(snipar.gtarray.gtarray method)
filter_bpg() (snipar.pgs.pgarray 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_covar() (snipar.slmm.LinearMixedModel static method)
fit_model() (in module snipar.lmm)
fit_models() (in module snipar.gwas)
fit_pgs_model() (in module snipar.pgs)
fit_snps_eff() (snipar.slmm.LinearMixedModel method)
forward_sim() (in module snipar.simulate)
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_parser_doc() (in module snipar.utilities)
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)
grad (snipar.slmm.LinearMixedModel property)
GradHessComponents (class in snipar.slmm)
grid_search_reml() (snipar.slmm.LinearMixedModel method)
gtarray (class in snipar.gtarray)
gts_matrix_chromosome() (in module snipar.scripts.gts_matrix)
H
h2eq_se() (in module snipar.pgs_am)
h2f_parse() (in module snipar.pgs)
haps_from_bgen() (in module snipar.simulate)
hessian (snipar.slmm.LinearMixedModel property)
I
imputation_test() (in module snipar.tests.test_imputation)
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)
K
k_se() (in module snipar.pgs_am)
L
ldscores_from_bed() (in module snipar.ld)
lik_and_grad() (in module snipar.lmm)
likelihood_and_gradient() (snipar.lmm.model method)
linear2coord() (in module snipar.utilities)
LinearMixedModel (class in snipar.slmm)
load_example_data() (in module snipar.example.snipar_example_data)
log (snipar.tests.utils.SniparTest attribute)
logger (snipar.slmm.LinearMixedModel attribute)
M
main() (in module snipar.example.simulate_phenotype)
(in module snipar.scripts.correlate)
(in module snipar.scripts.gts_matrix)
(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_and_fit_model() (in module snipar.pgs)
make_dynamic() (in module snipar.ibd)
make_grms() (in module snipar.pgs)
make_gts_matrix() (in module snipar.preprocess)
make_id_dict() (in module snipar.utilities)
map_from_bed() (in module snipar.map)
match_grm_ids() (in module snipar.slmm)
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.pgs_am
snipar.preprocess
snipar.read
snipar.read.bed
snipar.read.bgen
snipar.read.phenotype
snipar.scripts
snipar.scripts.correlate
,
[1]
snipar.scripts.gts_matrix
snipar.scripts.gwas
,
[1]
snipar.scripts.ibd
,
[1]
snipar.scripts.impute
,
[1]
snipar.scripts.pgs
,
[1]
snipar.scripts.simulate
,
[1]
snipar.simulate
snipar.slmm
snipar.tests.test_imputation
snipar.tests.test_impute
snipar.tests.test_impute_from_sibs
snipar.tests.test_sibreg
snipar.tests.utils
snipar.utilities
N
npg_am_adj() (in module snipar.pgs)
NumRangeAction (class in snipar.utilities)
O
open_bgen() (in module snipar.utilities)
opg_am_adj() (in module snipar.pgs)
optimize_model() (snipar.lmm.model method)
outarray_effect() (in module snipar.gwas)
outfile_name() (in module snipar.utilities)
P
P_attrs (snipar.slmm.LinearMixedModel property)
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)
P_varcomp_mats (snipar.slmm.GradHessComponents attribute)
P_y (snipar.slmm.GradHessComponents 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)
pgarray (class in snipar.pgs)
pgs (class in snipar.pgs)
pgs_cor_lik() (in module snipar.pgs)
pgs_corr_likelihood() (in module snipar.pgs)
pgs_corr_likelihood_fam() (in module snipar.pgs)
pgs_corr_matrix() (in module 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)
produce_next_gen_unlinked() (in module snipar.simulate)
R
r2_est() (in module snipar.ld)
r_se() (in module snipar.pgs_am)
random_design() (in module snipar.tests.test_sibreg)
random_mating_indices() (in module snipar.simulate)
read_bgen() (in module snipar.utilities)
read_covariates() (in module snipar.read.phenotype)
read_pgs() (in module snipar.pgs)
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)
read_weights() (in module snipar.pgs)
recurcive_append() (in module snipar.imputation.preprocess_data)
reml_loglik (snipar.slmm.LinearMixedModel property)
remove_zeros() (snipar.pgs.pgs method)
reweighted_estimate_cov() (in module snipar.correlate)
reweighted_estimate_var() (in module snipar.correlate)
rho_se() (in module snipar.pgs_am)
run_gcta_grm() (in module snipar.slmm)
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)
(snipar.pgs.pgarray method)
scipy_optimize() (snipar.slmm.LinearMixedModel method)
scores_from_ldsc() (snipar.correlate.sumstats method)
se_alpha_from_alpha() (in module snipar.pgs_am)
se_alpha_from_beta() (in module snipar.pgs_am)
se_check() (in module snipar.pgs_am)
se_v_eta_delta() (in module snipar.pgs_am)
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_effects() (in module snipar.simulate)
simulate_ests() (in module snipar.pgs_am)
simulate_first_gen() (in module snipar.simulate)
simulate_freqs() (in module snipar.simulate)
simulate_haplotypes() (in module snipar.simulate)
simulate_r_inf() (in module snipar.pgs)
simulate_recombinations() (in module snipar.simulate)
simulation_check() (in module snipar.pgs_am)
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.pgs_am
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
,
[1]
snipar.scripts.gts_matrix
module
snipar.scripts.gwas
module
,
[1]
snipar.scripts.ibd
module
,
[1]
snipar.scripts.impute
module
,
[1]
snipar.scripts.pgs
module
,
[1]
snipar.scripts.simulate
module
,
[1]
snipar.simulate
module
snipar.slmm
module
snipar.tests.test_imputation
module
snipar.tests.test_impute
module
snipar.tests.test_impute_from_sibs
module
snipar.tests.test_sibreg
module
snipar.tests.utils
module
snipar.utilities
module
SniparTest (class in snipar.tests.utils)
sp_solve_dense3d() (snipar.slmm.LinearMixedModel static method)
sp_solve_dense3d_lu() (snipar.slmm.LinearMixedModel static method)
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_alpha_mle() (snipar.tests.test_sibreg.test_regrnd_functions method)
test_dict_to_cmap() (snipar.tests.test_impute_from_sibs.TestSibImpute 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_hessian() (snipar.slmm.LinearMixedModel 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)
TestImpute (class in snipar.tests.test_impute)
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
V (snipar.slmm.LinearMixedModel property)
v_eta_delta() (in module snipar.pgs_am)
V_logdet (snipar.slmm.LinearMixedModel property)
V_lu (snipar.slmm.LinearMixedModel property)
varcomps (snipar.slmm.LinearMixedModel property)
Vinv_e (snipar.slmm.LinearMixedModel property)
Vinv_mat() (snipar.slmm.LinearMixedModel method)
Vinv_varcomp_mats (snipar.slmm.LinearMixedModel property)
Vinv_y (snipar.slmm.LinearMixedModel property)
Vinv_Z (snipar.slmm.LinearMixedModel property)
viterbi() (in module snipar.ibd)
W
write() (snipar.pgs.pgarray method)
write_2gen_adj_ests() (in module snipar.pgs)
write_estimates() (in module snipar.pgs)
write_genoarray() (in module snipar.scripts.gts_matrix)
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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