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ExprMethylCGH

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

Inputs

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.

Outputs

Name Type Description
statistics CSV Output contains separate signal-to-noise ratios for methylation and CGH grouping, an summary score for their joint effect, the error coefficient, and the adjacent p-values for each score.

Parameters

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 p-values.
strictChecks boolean false Enable additional checks for additive effect. See also strictLim.
strictLim float 0.05 P-value of significance for t-test if strictChecks=true. Disabled otherwise.

Test cases

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,
naLimit=0.15,

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

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