scoreSubpathways {CHRONOS} | R Documentation

## Evaluate subpathways using an interacting scorng scheme (IS) for each time point.

### Description

Evaluate subpathways using an interacting scorng scheme (IS) for each time point.

### Usage

    scoreSubpathways(subpathways, filters, measures, parameters, miRNAinteractions)

### Arguments

`subpathways` | Subpaths as returned from `extractLinearSubpathways` and `extractNonLinearSubpathways`.
`filters` | Named vector of filters used for subpathway evaluation. Values denote corresponding thresholds.
|  | pvalue | Statistical evaluation
|  | measures | Structural and functional evaluation
|  | subScore | mRNA-mRNA interaction scoring
|  | mirScore | miRNA-mRNA interaction scoring
`measures` | Subpathway structural and functional aspects as returned from `pathwayMeasures`.
`parameters` | C,K,T parameters of scoring scheme.
`miRNAinteractions` | An edgelist of miRNA-mRNA interactions used to override downloaded interactions from miRecords.

### Details

...

### Value

| subpathways | High ranking subpathways
| subScores | miRNA-subpathway scores
| mRNAScores | mRNA-mRNA scores for each subpathway and for each time point
| miRNAsOverSubpathway | High ranking miRNAs hitting each subpathway
| pValues | P-value of each subpathway
| filters | Filters used for the evaluation

### References

Jethava, V., Bhattacharyya, C., Dubhashi, D., & Vemuri, G. N. (2011). Netgem: Network embedded temporal generative model for gene expression data. BMC bioinformatics, 12(1), 327.

Kim,Y. et al. (2011). Principal network analysis: identification of subnetworks representing major dynamics using gene expression data. Bioinformatics, 27(3), 391-398

### Examples

    # Load extracted subpathways from toy data
    load(system.file('extdata', 'Examples//data.RData', package='CHRONOS'))

    # Import mRNA expressions
    mRNAexpr <- importExpressions(data=mRNAexpr, type='mRNA', org='hsa')

    # Score extracted linear subpathways
    filters       <- c('subScore'=0.4)
    linSubsScored <- scoreSubpathways(subpathways=linSubs, filters=filters)

[Package CHRONOS version 1.16.0 Index]