copaInt: copaInt

In OGSA: Outlier Gene Set Analysis

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)

Example output

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