| CLAC analysis for CGH-Miner {clac} | R Documentation |
These functions are desinged to be called by Excel Addin package CGH-Miner to perform CLAC analysis.
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)
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. |
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.
Pei Wang
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/