pynetcor 0.0.3

PyNetCor is a fast Python C++ extension for correlation and network analysis

pyNetCor

PyNetCor is a fast Python C++ extension for correlation and network analysis on high-dimensional datasets. It aims to serve as a scalable foundational package to accelerate large-scale computations.

Features

• Calculate correlation matrix using Pearson, Spearman, or Kendall methods
• Processing large-scale computation in chunks (larger than RAM)
• Find top-k and differential correlations between each row of two arrays
• Efficient P-value approximation and multiple testing correction
• Handle missing values
• Multi-thread

Installation

You can install pyNetCor using pip:

pip install pynetcor

Quick Start

Create Data

import numpy as np

features = 100000
sampes = 100
arr1 = np.random.random((features, samples))
arr2 = np.random.random((features, samples))

Calculate correlation matrix

Compute and return the full matrix at once.

from pynetcor.cor import corrcoef

# using 8 threads
# Pearson correlations between `arr1` and itself
cor_result = corrcoef(arr1, threads=8)

Compute the matrix in chunks and return an Iterator, recommended for large-scale analysis that exceed RAM.

from pynetcor.cor import chunked_corrcoef

# Calculate and return `chunk_size=1024` rows of the correlation matrix with each iteration.
cor_iter = chunked_corrcoef(arr1, chunk_size=1024, threads=8)
for cor_chunk_matrix in cor_iter:
    ...

Top-k correlation search

Identify the accurate top k correlations (Spearman correlation).

from pynetcor.cor import cor_topk

# top 1% correlations
cor_topk_result = cor_topk(arr1, method="spearman", k=0.001, threads=8)

# top 100 correlations
cor_topk_result = cor_topk(arr1, method="spearman", k=100, threads=8)

# Return a 2D array with 4 columns: [row_index, col_index, correlation, pvalue]

Top-k differential correlation search

Identify the accurate top k differences in correlation between pairs of features across two states or time points.

# Compute the pairwise correlations separately for `arr1` with `arr1`, and `arr2` with `arr2`, then identify the feature pairs with the largest difference
from pynetcor.cor import cor_topkdiff

# top 1% differential correlations
cor_topkdiff_result = cor_topkdiff(x1=arr1, y1=arr2, x2=arr1, y2=arr2, k=0.001, threads=8)

# top 100 differential correlations
cor_topkdiff_result = cor_topkdiff(x1=arr1, y1=arr2, x2=arr1, y2=arr2, k=100, threads=8)

# Return a 2D array with 5 columns: [row_index, col_index, diffCor, cor1, cor2]

P-value computation

Compute the P-values for correlations (Pearson or Spearman) using the Student's t-distribution. The approximation method is significantly faster than the classical method, with the absolute errors are nearly less than 1e-8.

from pynetcor.cor import corrcoef, pvalue_student_t
samples = arr1.shape[1]

# Generate the Pearson correlation matrix
cor_result = corrcoef(arr1, threads=8)

# P-value approximation
pvalue_result = pvalue_student_t(cor_result, df=samples-2, approx=True, threads=8)

# P-value classic
pvalue_result = pvalue_student_t(cor_result, df=samples-2, approx=False, threads=8)

Unified implementation for calculating correlations and P-values.

from pynetcor.cor import cortest, chunked_cortest

# Pearson correlation & P-value approximation
cortest_result = cortest(arr1, approx=True, threads=8)

# chunking computation, recommended for large-scale analysis that exceed RAM
for iter in chunked_cortest(arr1, approx=True, threads=8):
    for (row_index, col_index, correlation, pvalue) in iter:
        ...
        
# Return a 2D array with 4 columns: [row_index, col_index, correlation, pvalue]

Multiple testing correction: holm, hochberg, bonferroni, BH, BY.

from pynetcor.cor import cortest, chunked_cortest

# Pearson correlation & multiple testing correction
cortest_result = cortest(arr1, adjust_pvalue=True, adjust_method="BH", threads=8)

# chunking computation, recommended for large-scale analysis that exceed RAM
for iter in chunked_cortest(arr1, adjust_pvalue=True, adjust_method="BH", threads=8):
    for (row_index, col_index, correlation, pvalue) in iter:
        ...
        
# Return a 2D array with 5 columns: [row_index, col_index, correlation, pvalue, adjusted_pvalue]       

NOTE: chunked function only supports approximate adjusted P-value. PyNetCor utilizes approximation methods to achieve effective FDR control before computing all P-values.