platform.thresholds {pathprint} | R Documentation

## Pathway fingerprint threshold values

### 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

    platform.thresholds

### 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

    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]])

[Package pathprint version 1.16.0 Index]