R tools for the prediction of subset frequencies based on correlation


This set of R tools is an implementation the Subset Prediction from Enrichment Correlation (SPEC) method described in Bolen et al. (BMC Bioinformatics, 2011). This microarray deconvolution technique is designed to provide a simple, easy-to-implement alternative to standard deconvolution techniques, and is designed predict the cellular source for a pre-defined list of genes (i.e. a gene signature) using only data from total PBMCs. SPEC does not rely on the occurrence of cell subset-specific genes in the signature, but rather takes advantage of correlations with subset-specific genes across a set of samples. In addition, SPEC provides tools to compare datasets and calculate p-values for comparisons of interest.


SPEC has been implemented as a set of R scripts, available for download below.

SPEC code [zip]

Instructions for use:

To use SPEC, download the zip file, unzip, and follow the instructions in 'EXAMPLE_runSPEC.R'

Citing SPEC:

When including the results of the SPEC package in a publication, please cite the following paper:

Bolen CR, Uduman M, Kleinstein SH. Cell subset prediction for blood genomic studies. BMC Bioinformatics. 2011 Jun 24;12:258. PubMed ID: 21702940

For questions, comments, or requests, please contact Steven Kleinstein at steven.kleinstein@yale.edu