customCDFAnn {pathprint} | R Documentation

## Map probes to Entrez Gene IDs

### Description

Annotates an expression array with entrez gene IDs, averaging to resolve redundancies

### Usage

    customCDFAnn(data, ann)

### Arguments

`data` | expression dataframe
`ann` | annotation dataframe

### Details

Maps array probes to a unique list of Entrez Gene IDs. Rhe mean expression value is used for mutiple probes mapping to the same gene.

### Value

Returns a dataframe with a column for each column of the input data and rownames as unique entrez IDs.

### 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

`single.chip.enrichment`

### Examples

    require(pathprintGEOData)

    # load ALL dataset
    require(ALL)
    data(ALL)
    annotation(ALL)
    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)

    # The chip used was the Affymetrix Human Genome U95 Version 2 Array
    # The correspending GEO ID is GPL8300

    # Extract portion of the expression matrix
    ALL.exprs<-exprs(ALL)
    ALL.exprs.sub<-ALL.exprs[,1:5]

    # Annotate with Entrez Gene IDs,
    ALL.exprs.sub.entrez<-customCDFAnn(ALL.exprs.sub, chipframe$GPL8300$ann)
    head(ALL.exprs.sub.entrez)

[Package pathprint version 1.16.0 Index]