outCallRankE {OGSA} | R Documentation

## outCallRankE

### Description

Counts outliers by the Ghosh method and generates list objects with all outliers noted

### Usage

    outCallRankE (expressionSet, thres= 0.05, tail='right', corr=FALSE,
    offsets=NULL, names=NULL)

### Arguments

`expressionSet` | object containing Set of matrices of molecular data and phenotype data (1 for case, 0 for control)
`thres` | Alpha value
`tail` | A vector equal to the number of matrices with values left or right for where to find outliers
`corr` | Whether to correct for normal outliers
`offsets` | A vector equal to the number of matrices which sets the minimum value relative to normal to call outlier (corrected rank only)
`names` | A vector equal to the 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)

     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')

    outRankLRL <- outCallRankE(expressionSet, names=c('Expr', 'Meth', 'CNV'),
                                                              tail=tailLRL)

[Package OGSA version 1.12.0 Index]