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/