limix / cellregmap

CellRegMap: A statistical framework for mapping context-specific regulatory variants using scRNA-seq

limix

Genomic analyses require flexible models that can be adapted to the needs of the user.

Limix is a flexible and efficient linear mixed model library with interfaces to Python. It includes methods for

• Single-variant association and interaction testing
• Variance decompostion analysis with linear mixed models
• Association and interaction set tests
• Different utils for statistical analysis, basic i/o, and plotting.

We have an extensive documentation of the library. If you need further help or want to discuss anything related to limix, please, join our forum 💬 and have a chat with us 😃. In case you have found a bug, please, report it creating an issue.

Install

NOTE: We will be maintaining limix 2.0.x for a while, in case you find some missing feature in limix 3.0.x. If that is the case, please, type pip install "limix <3,>=2" in your terminal.

Installation is easy and works on macOS, Linux, and Windows:

pip install limix

If you already have Limix but want to upgrade it to the latest version:

pip install limix --upgrade

Interactive tutorials

• eQTL (requires limix 2.0.x)
• Struct-LMM (requires limix 2.0.x)

Running tests

After installation, you can test it

python -c "import limix; limix.test()"

as long as you have pytest.

Authors

• Christoph Lippert
• Danilo Horta
• Francesco Paolo Casale
• Oliver Stegle

License

This project is licensed under the Apache License License.

cellregmap's Issues

input error help

Hi CellRegMap team,

I have been trying to implement the workflow in my dataset, and I have been running into problems with the inputs. I keep getting the same error with the covariates matrix "ValueError: There are non-finite values in the covariates matrix." Even if I use a simple interaction vector with the length of ncells
"
n_cells = phenotype.shape[1]
W = ones((n_cells, 1))
"
So that takes me to believe the problem is arising somewhere else. I have searched for non-finite values and I cannot find them in my data.

Here are my inputs, maybe you can spot an error I am overlooking?

Thanks in advance,
Marliette

`
print(y)
array([[-0.52708307],
[-0.52708307],
[-0.52708307],
...,
[-0.52708307],
[ 2.54097084],
[-0.52708307]])

print(y.shape)
(9226, 1)

print(W)
array([[0],
[0],
[0],
...,
[1],
[1],
[1]])

print(W.shape)
(9226, 1)

print(C_gauss)
array([[-1.22191296, 0.02241402, 1.08167398, ..., -0.37086214,
1.31544543, -1.22191296],
[-0.02132711, 1.11544898, 1.22535893, ..., -0.37086214,
1.31544543, -1.22191296],
[-0.72577874, 0.599198 , 0.48035595, ..., -0.37086214,
1.31544543, -1.22191296],
...,
[ 2.29981396, -2.31538738, 3.03765002, ..., -0.37086214,
-0.23817144, -0.20600968],
[ 2.40800678, -2.31144121, 2.11206554, ..., -0.37086214,
-0.23817144, -0.20600968],
[ 2.96421393, -2.27745124, 2.24930127, ..., -0.37086214,
-0.23817144, -0.20600968]])

print(C_gauss.shape)
(9226, 16)

print(GG)
array([[2.],
[2.],
[2.],
...,
[2.],
[2.],
[2.]], dtype=float32)

prit(GG.shape)
(9226, 1)

print(hK)
array([[0., 0., 0., ..., 0., 0., 0.],
[0., 0., 0., ..., 0., 0., 0.],
[0., 0., 0., ..., 0., 0., 0.],
...,
[0., 0., 0., ..., 0., 0., 0.],
[0., 0., 0., ..., 0., 0., 0.],
[0., 0., 0., ..., 0., 0., 0.]])

print(hK.shape)
(9226, 364)
`

Is it possible to use this package on mouse data?

Hi,

I didn't find where you set the organism or use any reference database. Do you mind pointing out where I could change the organism from human to mouse? Thanks!