SPRINT

SPRINT Beta 3

The main change in SPRINT beta 0.3.0 is the addition of a clustering function to the SPRINT library of parallelized statistical R functions. It performs a Parallel Partitioning Around Medoids (PPAM) and is based on the pam() function from the cluster R package.

cluster

In addition, the implementation of the SPRINT pcor() function which performs the Pearson correlation in parallel has been extended to allow the correlation between two matrices.

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Functionality

The SPRINT function library contains four functions:

  • ppam(): a clustering Partition Around Medoid function
  • pmaxT(): a permutation test function
  • pcor(): a Pearson correlation function
  • ptest(): a simple 'Hello World!' function

Performance

The graph below was obtained on the UK National Supercomputing Service, HECToR, using up to 64 cores for dividing a dataset with 22,374 genes into 12 clusters.

ppam scaling