platform.thresholds {pathprint} | R Documentation |
Ternary threshold values for conversion of continuous geneset enrichment scores to discrete Pathway Fingerprint scores - high (1), mid (0), low (-1) for each geneset and platform covered by the Pathway Fingerprint.
platform.thresholds
Altschuler, G. M., O. Hofmann, I. Kalatskaya, R. Payne, S. J. Ho Sui, U. Saxena, A. V. Krivtsov, S. A. Armstrong, T. Cai, L. Stein and W. A. Hide (2013). "Pathprinting: An integrative approach to understand the functional basis of disease." Genome Med 5(7): 68.
require(pathprintGEOData) library(SummarizedExperiment) # load the data data(SummarizedExperimentGEO) data("platform.thresholds") # extract part of the GEO.fingerprint.matrix and GEO.metadata.matrix GEO.fingerprint.matrix = assays(geo_sum_data[,300000:350000])$fingerprint GEO.metadata.matrix = colData(geo_sum_data[,300000:350000]) head(platform.thresholds[[1]])