Integrates expression data with methylation and CGH data by using two label matrices of ones and zeros. Rows with missing values (NA) can be discarded based on the naLimit parameter. Values that are not 0, 1 or NA are ignored by the component and are not taken into account when computed the naLimit.
All three matrices must have equal dimensions. Moreover, column (samples) and rows are assumed to match; that is, the user must ensure that they both are in the correct order.
The CGHmet R package can be downloaded from here.
Version  1.1.1 

Bundle  microarray 
Categories  Integration 
Authors  Riku Louhimo (Riku.Louhimo@Helsinki.FI) 
Issue tracker  View/Report issues 
Source files  component.xml ExprMethylCGH.r 
Usage  Example with default values 
Name  Type  Mandatory  Description 

exprMatrix  CSV  Mandatory  Matrix of expression values. Contains the union of the samples in the label matrices. 
cghMatrix  CSV  Optional  Matrix of ones and zeros based on CGH measurements. 
methylMatrix  CSV  Optional  Matrix of ones and zeros based on methylation measurements. 
Name  Type  Description 

statistics  CSV  Output contains separate signaltonoise ratios for methylation and CGH grouping, an summary score for their joint effect, the error coefficient, and the adjacent pvalues for each score. 
Name  Type  Default  Description 

favorSynergetic  boolean  true  Defines whether genes with low frequency of overlapping '1' in cgh and methylation matrices are penalized. The default value favors genes where both cna and methylation work additively by setting epsilon=1 and using overlapping control samples. 
gainData  boolean  true  Defines whether label matrix values with ones correspond to gains/hypomethylation or losses/hypermethylation. 
naLimit  float  0.1  Percentage of missing values allowed in the expression matrix. 
permutation  int  1000  Number of permutations to perform to attain pvalues. 
strictChecks  boolean  false  Enable additional checks for additive effect. See also strictLim. 
strictLim  float  0.05  Pvalue of significance for ttest if strictChecks=true. Disabled otherwise. 
Test case  Parameters▼  IN exprMatrix 
IN cghMatrix 
IN methylMatrix 
OUT statistics 


case1  properties  exprMatrix  cghMatrix  methylMatrix  statistics  
permutation=100 

case2_Fail  (missing)  exprMatrix  cghMatrix  methylMatrix  (expecting failure)  
case3_noMet  properties  exprMatrix  cghMatrix  (missing)  statistics  
gainData=false, 

case4_empty  (missing)  exprMatrix  cghMatrix  (missing)  (expecting failure) 