platform.thresholds: Pathway fingerprint threshold values

Description Usage References Examples

Description

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.

Usage

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References

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.

Examples

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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]])

hidelab/pathprint documentation built on May 17, 2019, 3:57 p.m.