# CLAC analysis for CGH-Miner {clac}

### Description

These functions are desinged to be called by Excel Addin package CGH-Miner to perform CLAC analysis.

### Usage

clac.from.Excel(column.name, SampleID, Data, windowsize, FDR, log2trans, centerColumn, chromosomeOption) clac.preparenormal.Excel(inputdata) clac.onetumorarray.Excel(NormalResult, i) clac.finalsummary.Excel(NormalResult, CLAC.result) clac.PlotOneArray(inputdata, clac.result, Sample) clac.PlotConsensus(inputdata, clac.result, SampleIDPick)

### Arguments

- column.name
- string vector, provides the column names in the spread sheet.
- SampleID
- string vector, provides the sample ID for each CGH array.
- Data
- numeric matrix, contains the data read in from the spread sheet.
- windowsiz
- enumeric value, specifying the window size to carry out the average smooth.
- FDR
- numeric value between 0 and 1, specifying the desired fianl FDR for CLAC analysis.
- log2trans
- boolean variable, if TRUE, a log2 transform will be performed on
`Data`

. - centerColumn
- boolean variable, if TRUE, the columns of
`Data`

will be centered to zero. - chromosomeOption
- boolean variable. If False, the chromosome arms will be considered seperately. If true, two chormosome arms of one chromosome would be dealed together.
- inputdata
- retruned object from function
`clac.from.Excel`

. - NormalResult
- return object from function
`clac.preparenormal.Excel`

. - CLAC.result
- numeric matrix. First row records the estimated FDR for each array; second row records the
`alpha`

value for each array; all left rows records the result of CLAC analysis for each array. - Sample
- string variable, is the sample ID of one array.
- SampleIDPick
- string vector, is a subset of
`SampleID`

.

### Details

These functions are not to be used in RGui interface directly. For `clac`

functions in R, please see `clac.preparenormal.R`

, `clac.tumorarray.R, clac.PlotSingleArray.R, clac.PlotConsensus.R, clac.PlotAllArray.R`

.

### References

P. Wang, Y. Kim, J. Pollack, B. Narasimhan and R. Tibshirani, ?A method for calling gains and losses in array CGH data?, Biostatistics (accepted for publication 4/5/2004), available at http://www-stat.stanford.edu/~wp57/CGH-Miner/

Documentation reproduced from package clac, version 0.1-1. License: GPL (>= 2)