expressionSetPheno: expressionSetPheno

In OGSA: Outlier Gene Set Analysis

Description

Returns pheno info

Usage

expressionSetPheno(expressionSet)

Arguments

expressionSet

ExpressionSet object containing sets of data and phenotype information

Value

A list with all specific outlier calls for each molecular type in each case sample

References

Ochs, M. F., Farrar, J. E., Considine, M., Wei, Y., Meshinchi, S., & Arceci, R. J. (n.d.). Outlier Analysis and Top Scoring Pair for Integrated Data Analysis and Biomarker Discovery. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 1-1. doi:10.1109/tcbb.2013.153

Examples

data(ExampleData)

 library(Biobase)
# building the Annotated Data Frame
 phenoData <- AnnotatedDataFrame(
     data.frame(
        type = factor(x = pheno, labels = c("Control", "Case")),
         row.names = colnames(expr)
     )
 )
# build environment
 inputData <- list2env(list(exprs = expr, meth = meth, cnv = cnv))

# build expressionSet - other information can be added here
 expressionSet <- ExpressionSet(inputData, phenoData)

# retrieve phenotype data
 phenotype <- expressionSetPheno(expressionSet)

OGSA documentation built on April 28, 2020, 6:58 p.m.