Gene Pairs Analysis

Gene Pairs

Introduction

Gene pairs with a stable relationship in the sample, which can be gene expression data, or correlations between gene expression and drug sensitivity (or other data).

Install

Eigen

install eigen3

git clone https://gitlab.com/libeigen/eigen.git
cd eigen
mkdir build
cd build
cmake ..
make
make install

CLI11

install CLI11

git clone https://github.com/CLIUtils/CLI11.git
cd CLI11
mkdir build
cd build
cmake ..
make
make install

Local

There is no need to install CLI11 and eigen header files into the system library, use local header files directly.

Clone eigen and CLI11 library from github

git clone https://gitlab.com/libeigen/eigen.git
git clone https://github.com/CLIUtils/CLI11.git

Makefile

For MacOS, you should install libomp and llvm

brew install llvm
brew install libomp

Check if the library is installed successfully

brew info llvm
brew info libomp

modify Makefile, Replace with the path to the corresponding library on your computer

INCLUDE = -I /usr/local/include/eigen3 -I /usr/local/include -I /usr/local/opt/libomp/include
LIBRARY = -L /usr/local/opt/llvm/lib
CXXFLAGS = -std=c++17 -Xclang -fopenmp -lomp -O3 $(LIBRARY) $(INCLUDE)

For Linux

modify Makefile, If the system supports openmp, modify it directly

INCLUDE = -I ./eigen -I ./CLI11/include
CXXFLAGS = -std=c++17 -fopenmp -O3 $(INCLUDE)

Finally, compile the program using make

Usage

The program contains two subcommands, which are used to calculate feature pairs with stable size relationships and feature pairs with correlated relationships.

./gene_pairs                                                                                                                                     
program:./gene_pairs

Usage: ./gene_pairs [OPTIONS] SUBCOMMAND

Options:
  -h,--help                             Print this help message and exit

Subcommands:
  stable                                Find feature pairs that have a stable relationship in one type of sample and a reversed relationship in another type of sample.
  corr                                  Find feature pairs whose expression relationships (addition, subtraction, multiplication, division) are highly correlated with other features.

For identifying feature pairs with stable size relationships

./gene_pairs stable                                                                                                                              
Find feature pairs that have a stable relationship in one type of sample and a reversed relationship in another type of sample.
Usage: ./gene_pairs stable [OPTIONS]

Options:
  -h,--help                             Print this help message and exit
  -i,--input TEXT:FILE REQUIRED         Feature data file.
  -t,--target TEXT:FILE                 Other features data file.
  -o,--output TEXT                      Output filename.
  --ratio FLOAT [0.9]                   The ratio of feature a > feature b in all samples.
  --revRatio FLOAT [0.7]                The ratio of feature a < feature b in another samples.
  --threads UINT [2]                    Number of threads used.
  --block UINT                          Data blocks processed by each thread, defaults to the size of the column.

For identifying relevant feature pairs

./gene_pairs corr                                                                                                                                
Find feature pairs whose expression relationships (addition, subtraction, multiplication, division) are highly correlated with other features.
Usage: ./gene_pairs corr [OPTIONS]

Options:
  -h,--help                             Print this help message and exit
  -i,--input TEXT:FILE REQUIRED         Feature data file.
  -t,--target TEXT:FILE                 Other features data file.
  -o,--output TEXT                      Output filename.
  -m,--method TEXT [pearson]            Correlation method, pearson/spearman/kendall.
  -a,--operation TEXT [subtract]        Operations(add/subtract/multiply/divide) between features.
  --type TEXT [common]                  Analysis type, common/cross/pairs.
  --cutoff FLOAT [0.3]                  Correlation coefficient threshold.
  --threads UINT [2]                    Number of threads used.
  --block UINT                          Data blocks processed by each thread, defaults to the size of the column.

dxsbiocc/gene_pairs