consensusDistance {pathprint} | R Documentation

## Calculate a distribution of distances from a consensus fingerprint

### Description

Calculates the distance from a consensus for a series of pathway fingerprints, accounting only for significantly high or low (-1 or 1) pathways in the consensus

### Usage

    consensusDistance(consensus, fingerprintframe)

### Arguments

`consensus` | consensus fingerprint
`fingerprintframe` | dataframe of sample fingerprints from which the distance will be calculated

### Details

The consensus fingerprint can be calculated using `consensusFingerprint` or alternatively can be a single fingerprint vector

### Value

A dataframe with rows corresponding to each sample contained in the fingerprintframe with the following columns

`distance` | Manhattan distance of sample from the consensus fingerprint, scaled by the maximum possible distance
`pvalue` | p-value representing the probabilty that the samples are not phenotypically matched. N.B. this is only valid when the fingerprint frame represents a sufficiently broad coverage of phenotypes, e.g. the GEO corpus. This p-value is based on an assumption that the distances are normally distributed

### 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

`consensusFingerprint`

### 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
    # create consensus fingerprint for pluripotent samples
    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")

[Package pathprint version 1.10.4 Index]