consensusFingerprint: Construct a consensus fingerprint

In hidelab/pathprint: Pathway fingerprinting for analysis of gene expression arrays

Description

Produces a pathway fingerprint that represents the consensus of a series of pathway fingerprints, according to a user-defined threshold

Usage

consensusFingerprint(fingerprintframe, threshold)

Arguments

fingerprintframe	matrix of fingerprints from which the consensus will be calculated
threshold	threshold value (between 0 and 1)

Details

For each pathway the mean fingerprint score, m, is calculated, and the consensus defined as
+1 if m > threshold
-1 if m < threshold
0 otherwise

Value

Vector of consensus pathway fingerprint scores with names corresponding to pathways

Author(s)

Gabriel Altschuler

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.

See Also

consensusDistance

Examples

require(pathprintGEOData)
library(SummarizedExperiment)

# load  the data
data(SummarizedExperimentGEO)

ds = c("chipframe", "genesets","pathprint.Hs.gs",
    "platform.thresholds","pluripotents.frame")
data(list = ds)

# 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])

# free up space by removing the geo_sum_data object
remove(geo_sum_data)

# Extract common GSMs since we only loaded part of the geo_sum_data object
common_GSMs <- intersect(pluripotents.frame$GSM,colnames(GEO.fingerprint.matrix))

# search for pluripotent arrays
# load fingerprint matrix and pluripotent reference

# create consensus fingerprint
pluripotent.consensus<-consensusFingerprint(
    GEO.fingerprint.matrix[,common_GSMs], threshold=0.9)

# calculate distance from the pluripotent consensus
geo.pluripotentDistance<-consensusDistance(pluripotent.consensus,
    GEO.fingerprint.matrix)

# plot histograms
par(mfcol = c(2,1), mar = c(0, 4, 4, 2))
geo.pluripotentDistance.hist<-hist(geo.pluripotentDistance[,"distance"],
    nclass = 50, xlim = c(0,1), main = "Distance from pluripotent consensus")
par(mar = c(7, 4, 4, 2))
hist(geo.pluripotentDistance[pluripotents.frame$GSM, "distance"],
    breaks = geo.pluripotentDistance.hist$breaks, xlim = c(0,1), 
    main = "", xlab = "above: all GEO, below: curated pluripotent samples")

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