The phyper library (pronounced "viper") computes the cumulative probability for a hypergeometric distribution, intended for testing overrepresentation of pathways/signatures within the set of marker genes. The interface is based on R's stats::phyper() function, with support for (log-transformed) probabilities of either tail.

#include "phyper/phyper.hpp"
phyper::Options opt;
opt.upper_tail = true;
opt.log = false;
// Equivalent to stats::phyper(5-1, 20, 10000, 100, lower.tail=FALSE)
phyper::compute(
    /* number of marker genes from the pathway */ 5, 
    /* number of genes in the pathway */ 20, 
    /* number of genes not in the pathway */ 10000,
    /* number of marker genes */ 100,
    opt
);

Note that the upper-tailed cumulative probability returned by phyper::compute() includes the probability mass of the observed number of marker genes in the pathway. This means that it can be directly used as the overrepresentation p-value for the pathway. For comparable results from stats::phyper(), users should subtract 1 from the q= argument as inicated above.

Check out the reference documentation for more details.

If you're using CMake, you just need to add something like this to your CMakeLists.txt:

include(FetchContent)
FetchContent_Declare(
  phyper
  GIT_REPOSITORY https://github.com/libscran/phyper
  GIT_TAG master # or any version of interest
)
FetchContent_MakeAvailable(phyper)

Then you can link to phyper to make the headers available during compilation:

# For executables:
target_link_libraries(myexe libscran::phyper)
# For libaries
target_link_libraries(mylib INTERFACE libscran::phyper)

find_package(libscran_phyper CONFIG REQUIRED)
target_link_libraries(mylib INTERFACE libscran::phyper)

To install the library, use:

mkdir build && cd build
cmake .. -DNENESUB_TESTS=OFF
cmake --build . --target install

If you're not using CMake, the simple approach is to just copy the files in include/ - either directly or with Git submodules - and include their path during compilation with, e.g., GCC's -I.T