limix
api
Table of contents
Installation
Command line interface
I/O module
Heritability estimation
Quality control
Quantitative trait locus
Shell utilities
Statistics
Tutorials
API reference
Developers
limix
Docs
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Index
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Index
_
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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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K
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L
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M
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N
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P
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Q
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R
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S
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U
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V
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Y
_
__init__() (limix.io.hdf5.fetcher method)
(limix.plot.ConsensusCurve method)
(limix.qtl.QTLModel method)
(limix.stats.Chi2Mixture method)
_normalise_dataset() (in module limix._dataset)
A
add() (limix.plot.ConsensusCurve method)
allele_expectation() (in module limix.stats)
allele_frequency() (in module limix.stats)
alt_lmls (limix.qtl.QTLModel attribute)
B
box_aspect() (in module limix.plot)
boxcox() (in module limix.qc)
C
Chi2Mixture (class in limix.stats)
compute_dosage() (in module limix.stats)
compute_maf() (in module limix.qc)
confusion_matrix() (in module limix.stats)
consensus() (limix.plot.ConsensusCurve method)
ConsensusCurve (class in limix.plot)
count_missingness() (in module limix.qc)
covariance_matrices (limix.glmm.GLMMComposer attribute)
D
decomp() (limix.glmm.GLMMComposer method)
download() (in module limix.sh)
E
effsizes_se() (in module limix.stats)
empirical_pvalues() (in module limix.stats)
estimate() (in module limix.her)
estimate_chi2mixture() (limix.stats.Chi2Mixture method)
extract() (in module limix.sh)
F
fetch() (in module limix.io.hdf5)
(limix.io.hdf5.fetcher method)
fetch_dosage() (in module limix.io.plink)
fetcher (class in limix.io.hdf5)
filehash() (in module limix.sh)
fit() (limix.glmm.GLMMComposer method)
fixed_effects (limix.glmm.GLMMComposer attribute)
G
get_pyplot() (in module limix.plot)
I
image() (in module limix.plot)
indep_pairwise() (in module limix.qc)
K
kinship() (in module limix.plot)
L
likname (limix.glmm.GLMMComposer attribute)
linear_kinship() (in module limix.stats)
lml() (limix.glmm.GLMMComposer method)
load_dataset() (in module limix.plot)
lrt_pvalues() (in module limix.stats)
M
manhattan() (in module limix.plot)
mean_impute() (in module limix.qc)
mean_standardize() (in module limix.qc)
multipletests() (in module limix.stats)
N
normal() (in module limix.plot)
normalise_covariance() (in module limix.qc)
null_covariate_effsizes (limix.qtl.QTLModel attribute)
null_lml (limix.qtl.QTLModel attribute)
P
pca() (in module limix.plot)
(in module limix.stats)
power() (in module limix.plot)
Q
qqplot() (in module limix.plot)
QTLModel (class in limix.qtl)
quantile_gaussianize() (in module limix.qc)
R
read() (in module limix.io.bgen)
(in module limix.io.csv)
(in module limix.io.gen)
(in module limix.io.npy)
(in module limix.io.plink)
read_limix() (in module limix.io.hdf5)
read_phenotype() (in module limix.io.bimbam)
regress_out() (in module limix.qc)
remove() (in module limix.sh)
remove_dependent_cols() (in module limix.qc)
S
save() (in module limix.io.npy)
scan() (in module limix.qtl)
see() (in module limix.io.csv)
(in module limix.io.hdf5)
(in module limix.io.npy)
see_bed() (in module limix.io.plink)
see_kinship() (in module limix.io.plink)
see_phenotype() (in module limix.io.bimbam)
sf() (limix.stats.Chi2Mixture method)
show() (in module limix.plot)
U
unique_variants() (in module limix.qc)
V
variant_effsizes (limix.qtl.QTLModel attribute)
variant_effsizes_se (limix.qtl.QTLModel attribute)
variant_pvalues (limix.qtl.QTLModel attribute)
Y
y (limix.glmm.GLMMComposer attribute)
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