copaInt {OGSA} | R Documentation

## copaInt

### Description

Counts outliers by Tibshirani-Hastie method by calling outCount after setting up list or by rank outlier method by calling outRank

### Usage

    copaInt(dataSet, phenotype, tails, thres = 0.05, method='Tibshirani',
    corr=FALSE, offsets=NULL)

### Arguments

`dataSet` | Set of matrices of molecular data
`phenotype` | Vector of 1 for case, 0 for control
`tails` | Vector equal to number of matrices with values left or right for where to find outliers
`thres` | alpha value
`method` | Tibshirani , Rank
`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)

### Value

A vector with outlier counts by gene

### 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)

    #Set up phenotype
    phenotype <- pheno
    names(phenotype) <- colnames(cnv)

    #set up values for expr-meth-cnv in that order
    tailLRL <- c('left', 'right', 'left')

    #setup dataSet
    dataSet <- list(expr, meth, cnv)

    tibLRL <- copaInt(dataSet, phenotype, tails=tailLRL)

[Package OGSA version 1.12.0 Index]