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CLAC analysis for CGH-Miner {clac}

R Functions for Excel Addin Packgage CGH-Miner
Package: 
clac
Version: 
0.1-1

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/

Author(s)

Pei Wang

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