platform.thresholds: Pathway fingerprint threshold values
In hidelab/pathprint: Pathway fingerprinting for analysis of gene expression arrays
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
1
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])$fingerprint
GEO.metadata.matrix = colData(geo_sum_data[,300000:350000])
head(platform.thresholds[[1]])
hidelab/pathprint documentation built on May 17, 2019, 3:57 p.m.
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Description Usage References Examples
Description
Ternary threshold values for conversion of continuous geneset enrichment scores to discrete Pathway Fingerprint scores - high (1), mid (0), low (-1) for each geneset and platform covered by the Pathway Fingerprint.
Usage
1 |
References
Altschuler, G. M., O. Hofmann, I. Kalatskaya, R. Payne, S. J. Ho Sui, U. Saxena, A. V. Krivtsov, S. A. Armstrong, T. Cai, L. Stein and W. A. Hide (2013). "Pathprinting: An integrative approach to understand the functional basis of disease." Genome Med 5(7): 68.
Examples
1 2 3 4 5 6 7 8 9 10 11 12 | require(pathprintGEOData)
library(SummarizedExperiment)
# load the data
data(SummarizedExperimentGEO)
data("platform.thresholds")
# extract part of the GEO.fingerprint.matrix and GEO.metadata.matrix
GEO.fingerprint.matrix = assays(geo_sum_data[,300000:350000])$fingerprint
GEO.metadata.matrix = colData(geo_sum_data[,300000:350000])
head(platform.thresholds[[1]])
|
R Package Documentation
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