README.md

In hui-tony-zk/distanceParallel: Creates distance matrix with custom distance function in parallel

distanceParallel, a package to calculate distance matrixes with arbitrary distance functions and parallelized with foreach frontend and the doMC backend

If you do ?dist you'll see that there are only a few (but common) methods for calculating distances. However, if you want to compare between two samples and you need a custom distance function, well you're out of luck.

This package is designed to do just that - calculate arbitrary distances between all pairwise comparisosn of either rows or columns of a matrix. Using foreach and doMC, these calculations are parallized for faster runtimes.

Warning: due to the usage of doMC, this package does not work on windows machines

Main functions

divide_cores()

This function is used within create_pairwise_comparisons() to split up the total amount of calculations evenly across all cores, which reduces "overhead" time spent on spawning new processes

create_pairwise_comparisons()

This function creates all pairwise combinations with comb, and loops over all of these combinations and applies a custom distance function (defaults to euclidian distance). This returns a data.frame containg the two samples that were matched together and their distance.

create_distance_matrix()

Finally, this function converts the data.frame into a distance matrix using tidyr::spread and as.dist()

hui-tony-zk/distanceParallel documentation built on May 17, 2019, 9:13 p.m.