limix
latest
Table of contents
Install
I/O module
Quality control
Quantitative trait locus
Variance decomposition
Heritability estimation
Plotting
Command line interface
Statistics
Model
API reference
limix
»
Index
Edit on GitHub
Index
_
|
A
|
B
|
C
|
D
|
E
|
F
|
G
|
I
|
K
|
L
|
M
|
N
|
O
|
P
|
Q
|
R
|
S
|
U
|
V
|
X
_
__init__() (limix.plot.ConsensusCurve method)
(limix.stats.Chi2Mixture method)
(limix.vardec.VarDec method)
A
A (limix.model.lmm.Kron2Sum property)
(limix.model.mean.KronMean property)
allele_expectation() (in module limix.stats)
allele_frequency() (in module limix.stats)
AX (limix.model.mean.KronMean property)
B
B (limix.model.lmm.Kron2Sum property)
(limix.model.mean.KronMean property)
beta (limix.model.glmm.GLMMExpFam property)
(limix.model.glmm.GLMMNormal property)
(limix.model.lmm.Kron2Sum property)
(limix.model.lmm.LMM property)
beta_covariance (limix.model.lmm.Kron2Sum property)
(limix.model.lmm.LMM property)
box_aspect() (in module limix.plot)
boxcox() (in module limix.qc)
C
C0 (limix.model.cov.Kron2SumCov property)
(limix.model.lmm.Kron2Sum property)
C1 (limix.model.cov.Kron2SumCov property)
(limix.model.lmm.Kron2Sum property)
Chi2Mixture (class in limix.stats)
compute_dosage() (in module limix.stats)
compute_maf() (in module limix.qc)
confusion_matrix() (in module limix.stats)
ConsensusCurve (class in limix.plot)
count_missingness() (in module limix.qc)
covariance() (limix.model.glmm.GLMMExpFam method)
(limix.model.lmm.Kron2Sum method)
(limix.model.lmm.LMM method)
D
D (limix.model.cov.Kron2SumCov property)
delta (limix.model.lmm.LMM property)
dim (limix.model.cov.EyeCov property)
download() (in module limix.sh)
E
effsizes (limix.model.mean.LinearMean property)
eigh() (limix.model.cov.FreeFormCov method)
empirical_pvalues() (in module limix.stats)
estimate() (in module limix.her)
ExpFamGP (class in limix.model.ggp)
extract() (in module limix.sh)
EyeCov (class in limix.model.cov)
F
filehash() (in module limix.sh)
fit() (limix.model.ggp.ExpFamGP method)
(limix.model.glmm.GLMMExpFam method)
(limix.model.gp.GP method)
(limix.model.lmm.Kron2Sum method)
(limix.model.lmm.LMM method)
fix() (limix.model.cov.FreeFormCov method)
(limix.model.cov.LinearCov method)
(limix.model.cov.LRFreeFormCov method)
(limix.model.glmm.GLMMExpFam method)
(limix.model.glmm.GLMMNormal method)
(limix.model.lmm.LMM method)
fix_offset() (limix.model.mean.OffsetMean method)
FreeFormCov (class in limix.model.cov)
G
G (limix.model.cov.Kron2SumCov property)
Ge (limix.model.cov.Kron2SumCov attribute)
get_fast_scanner() (limix.model.glmm.GLMMNormal method)
(limix.model.lmm.Kron2Sum method)
(limix.model.lmm.LMM method)
get_pyplot() (in module limix.plot)
GivenCov (class in limix.model.cov)
GLMMExpFam (class in limix.model.glmm)
GLMMNormal (class in limix.model.glmm)
GP (class in limix.model.gp)
gradient() (limix.model.cov.EyeCov method)
(limix.model.cov.FreeFormCov method)
(limix.model.cov.GivenCov method)
(limix.model.cov.Kron2SumCov method)
(limix.model.cov.LinearCov method)
(limix.model.cov.LRFreeFormCov method)
(limix.model.cov.SumCov method)
(limix.model.glmm.GLMMExpFam method)
(limix.model.lmm.Kron2Sum method)
(limix.model.lmm.LMM method)
(limix.model.mean.KronMean method)
(limix.model.mean.LinearMean method)
(limix.model.mean.OffsetMean method)
(limix.model.mean.SumMean method)
gradient_dot() (limix.model.cov.Kron2SumCov method)
I
image() (in module limix.plot)
indep_pairwise() (in module limix.qc)
iscan() (in module limix.qtl)
K
kinship() (in module limix.plot)
Kron2Sum (class in limix.model.lmm)
Kron2SumCov (class in limix.model.cov)
KronMean (class in limix.model.mean)
L
L (limix.model.cov.FreeFormCov property)
(limix.model.cov.LRFreeFormCov property)
LdKL_dot() (limix.model.cov.Kron2SumCov method)
Lh (limix.model.cov.Kron2SumCov property)
linear_kinship() (in module limix.stats)
LinearCov (class in limix.model.cov)
LinearMean (class in limix.model.mean)
listen() (limix.model.cov.FreeFormCov method)
(limix.model.cov.Kron2SumCov method)
(limix.model.cov.LRFreeFormCov method)
lml() (limix.model.ggp.ExpFamGP method)
(limix.model.gp.GP method)
(limix.model.lmm.Kron2Sum method)
(limix.model.lmm.LMM method)
LMM (class in limix.model.lmm)
load_dataset() (in module limix.plot)
logdet() (limix.model.cov.FreeFormCov method)
(limix.model.cov.Kron2SumCov method)
logdet_gradient() (limix.model.cov.Kron2SumCov method)
LRFreeFormCov (class in limix.model.cov)
lrt_pvalues() (in module limix.stats)
Lu (limix.model.cov.FreeFormCov property)
(limix.model.cov.LRFreeFormCov property)
Lx (limix.model.cov.Kron2SumCov property)
M
M (limix.model.lmm.Kron2Sum property)
manhattan() (in module limix.plot)
mean() (limix.model.lmm.Kron2Sum method)
(limix.model.lmm.LMM method)
mean_impute() (in module limix.qc)
mean_standardize() (in module limix.qc)
multipletests() (in module limix.stats)
multivariate_normal() (in module limix.stats)
N
ncovariates (limix.model.lmm.Kron2Sum property)
(limix.model.lmm.LMM property)
normal() (in module limix.plot)
normalise_covariance() (in module limix.qc)
nparams (limix.model.cov.FreeFormCov property)
(limix.model.cov.Kron2SumCov property)
(limix.model.cov.LRFreeFormCov property)
(limix.model.mean.KronMean property)
nsamples (limix.model.lmm.Kron2Sum property)
(limix.model.lmm.LMM property)
ntraits (limix.model.lmm.Kron2Sum property)
O
offset (limix.model.mean.OffsetMean property)
OffsetMean (class in limix.model.mean)
P
pca() (in module limix.plot)
(in module limix.stats)
posteriori_covariance() (limix.model.glmm.GLMMExpFam method)
posteriori_mean() (limix.model.glmm.GLMMExpFam method)
power() (in module limix.plot)
Q
qqplot() (in module limix.plot)
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)
remove() (in module limix.sh)
remove_dependent_cols() (in module limix.qc)
S
scale (limix.model.cov.EyeCov property)
(limix.model.cov.GivenCov property)
(limix.model.cov.LinearCov property)
(limix.model.lmm.LMM property)
scan() (in module limix.qtl)
shape (limix.model.cov.FreeFormCov property)
(limix.model.cov.LRFreeFormCov property)
show() (in module limix.plot)
solve() (limix.model.cov.Kron2SumCov method)
SumCov (class in limix.model.cov)
SumMean (class in limix.model.mean)
U
unfix() (limix.model.cov.FreeFormCov method)
(limix.model.cov.LinearCov method)
(limix.model.cov.LRFreeFormCov method)
(limix.model.glmm.GLMMExpFam method)
(limix.model.glmm.GLMMNormal method)
(limix.model.lmm.LMM method)
unfix_offset() (limix.model.mean.OffsetMean method)
unique_variants() (in module limix.qc)
V
v0 (limix.model.lmm.LMM property)
v1 (limix.model.lmm.LMM property)
value() (limix.model.cov.EyeCov method)
(limix.model.cov.FreeFormCov method)
(limix.model.cov.GivenCov method)
(limix.model.cov.Kron2SumCov method)
(limix.model.cov.LinearCov method)
(limix.model.cov.LRFreeFormCov method)
(limix.model.cov.SumCov method)
(limix.model.glmm.GLMMNormal method)
(limix.model.lmm.Kron2Sum method)
(limix.model.lmm.LMM method)
(limix.model.mean.KronMean method)
(limix.model.mean.LinearMean method)
(limix.model.mean.OffsetMean method)
(limix.model.mean.SumMean method)
VarDec (class in limix.vardec)
X
X (limix.model.cov.LinearCov property)
(limix.model.lmm.Kron2Sum property)
(limix.model.lmm.LMM property)
(limix.model.mean.KronMean property)
(limix.model.mean.LinearMean property)
Read the Docs
v: latest
Versions
latest
stable
Downloads
On Read the Docs
Project Home
Builds