customCDFAnn: Map probes to Entrez Gene IDs

In pathprint: Pathway fingerprinting for analysis of gene expression arrays

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)

pathprint documentation built on April 28, 2020, 7:54 p.m.