limix/cellregmap

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

CellRegMap

Cellular Regulatory Map (CellRegMap) is a linear mixed model approach to perform multi-context eQTL mapping by leveraging single cell RNA sequencing (scRNA-seq) data. It is related to the previously proposed StructLMM but importantly it can account for sample structure, including population structure and repeated observations for the same samples, e.g., multiple cells for the same donor.

The CellRegMap model and its applications to both real and simulated data are described in the CellRegMap manuscript.

For more instructions and tutorials to facilitate usage of the package visit our website!

Install

From your command line, enter

python3 -m pip install cellregmap

in your command line.

Development

To install it in development mode, enter

git clone https://github.com/limix/CellRegMap.git
cd CellRegMap
python3 -m pip install -e .

in your command line.

Installation using a Docker image

If you use Docker, you can also pull the pre-build image from dockerhub.

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!