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Up: Component summary
Component
ExprMethylCGHIntegrates 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 DNA Methylation |
| 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 |
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| case2_Fail | (missing) | exprMatrix | cghMatrix | methylMatrix | (expecting failure) | |
| case3_noMet | properties | exprMatrix | cghMatrix | (missing) | statistics | |
|
gainData=false, |
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| case4_empty | (missing) | exprMatrix | cghMatrix | (missing) | (expecting failure) | |