ERStruct 0.2.1
Determine number of principle components based on sequencing data
License: MIT
Keywords: Population structure,Principal component,Random matrix theory,Sequencing data,Spectral analysis


# ERstruct - Official Python Implementation

A Python package for inferring the number of top informative PCs that capture population structure based on genotype information.

## Requirements for Data File
1. Data files must be of numpy array `.npy` format. Users can convert VCF (variant call format) file in to numpy array via `vcfnp` package： https://pypi.org/project/vcfnp/, and convert bgen  file in to numpy array via `bgen-reader` package： https://pypi.org/project/bgen-reader/.
2. The data matrix must with 0,1,2 and/or NaN (for missing values) entries only. Noting that our package imputes all the missing data (NaN) by 0. Users may perform other types of imputations beforehand.
3. The rows represent individuals and columns represent markers. If there are more than one data files, the data matrix inside must with the same number of rows.




## Dependencies
ERStruct depends on `numpy`, `torch` and `joblib`.

## Installation
Users can install `ERStruct` by running the command below in command line:
```commandline
pip install ERStruct
```

## Parameters
```
erstruct(n, path, rep, alpha, cpu_num=1, device_idx="cpu", varm=2e8, Kc=-1)
```

**n** *(int)* - total number of individuals in the study

**path** *(str)* - the path of data file(s)

**rep** *(int)* - number of simulation times for the null distribution (set to `5000` by default). We recommend to use `rep` between `2/alpha` and `5/alpha`.

**alpha** *(float)* - significance level, can be either a scaler or a vector (set to `1e-3` by default)

**Kc** *(int)* - a coarse estimate of the top PCs number (set to `-1` by default, denoting `Kc = floor(n/10)` when the algorithm running)

**cpu_num** *(int)* - optional, number of CPU cores to be used for parallel computing. (set to `1` by default)

**device_idx** *(str)* - device you are using, "cpu" pr "gpu". (set to `"cpu"` by default)

**varm** *(int)*: - Allocated memory (in bytes) of GPUs for computing. When device_idx is set to "gpu", the varm parameter can be specified to increase the computational speed by allocating the required amount of memory (in bytes) to the GPU.  (set to `2e+8` by default)

## Examples
Import ERStruct algorithm
```
from ERStruct import erstruct
```

Download sample dataset (the dataset consists of chromosome 21 and chromosome 22 information for 500 individuals obtained 
    from sequencing data of the 1000 Genomes Project.):
```angular2html
from ERStruct import download_sample
download_sample()
```

Run ERStruct algorithm on sample dataset with CPUs:
```commandline
test = erstruct(500, ['chr21.npy', 'chr22.npy'], 1000, 5e-3, cpu_num=1, device_idx="cpu")
K = test.run()
```
Run ERStruct algorithm on sample dataset with GPUs:
```commandline
test = erstruct(500, ['chr21.npy', 'chr22.npy'], 1000, 5e-3, device_idx="gpu", varm=2e8)
K = test.run()
```


## Other Details
Please refer to our paper
> [ERStruct: A Python Package for Inferring the Number of Top Principal Components from Whole Genome Sequencing Data](https://www.biorxiv.org/content/10.1101/2022.08.15.503962v2)

For details of the ERStruct algorithm:
> [ERStruct: An Eigenvalue Ratio Approach to Inferring Population Structure from Sequencing Data](https://www.researchgate.net/publication/350647012_ERStruct_An_Eigenvalue_Ratio_Approach_to_Inferring_Population_Structure_from_Sequencing_Data)

If you have any question, please contact the email eciel@connect.hku.hk.