outCallTibE {OGSA} | R Documentation

## outCallTibE

### Description

Counts outliers by the Tibshirani and Hastie method and generates a list object with all outliers noted

### Usage

    outCallTibE (expressionSet, tail='right', corr=FALSE, names=NULL)

### Arguments

`expressionSet` | ExpressionSet object containing sets of data and phenotype information
`tail` | Vector equal to number of matrices with values 'left' or 'right' for where to find outliers
`corr` | whether to correct for normal outliers ONLY for compatibility, since method does not allow determining specific changes in cases, it will just print message if corr = TRUE
`names` | Vector equal to number of matrices to name molecular type of data (e.g., 'CNV').

### 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

D. Ghosh. (2010). Discrete Nonparametric Algorithms for Outlier Detection with Genomic Data. J. Biopharmaceutical Statistics, 20(2), 193-208.

### Examples

    data(ExampleData)
    data('KEGG_BC_GS')

     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)

    # set up values for for the tails in the order that they are exported, for example:
    tailLRL <- c('left', 'right', 'left')

    outTibLRL <- outCallTibE(expressionSet, names=c('Expr', 'Meth', 'CNV'), tail=tailLRL)

[Package OGSA version 1.16.0 Index]