CHRONOSrun {CHRONOS} | R Documentation

## Default run of CHRONOS

### Description

Default run of CHRONOS

### Usage

    CHRONOSrun(mRNAexp, mRNAlabel, miRNAexp, pathType, subType, measures,
        thresholds, org, export, verbose, miRNAinteractions)

### Arguments

`mRNAexp` | mRNA expressions filename located in CHRONOS/extdata/Input
`mRNAlabel` | mRNA nomenclature (for supported types see `convertNomenclature`)
`miRNAexp` | miRNA expressions filename located in CHRONOS/extdata/Input
`pathType` | Pathway type ('Metabolic', 'Non-Metabolic', 'All' or vector of pathway ids)
`subType` | Subpathway type ('Linear', 'Non-Linear', 'All')
`measures` | Include subpathway structural and functional aspects ('TRUE', 'FALSE')
`thresholds` | Subscore, mirscore and p-value thresholds c('pvalue'=pvalue, 'subscore'=subscore, 'mirscore'=mirscore)
`org` | KEGG organism identifier
`export` | Export file type ('.xlsx', '.txt')
`verbose` | Show informative messages (TRUE/FALSE).
`miRNAinteractions` | Edgelist of miRNA-mRNA interactions.

### Details

- Imports gene and miRNA expressions from CHRONOS/extdata/Input/<mRNAexpFile>.txt
  and CHRONOS/extdata/Input/<miRNAexpFile>.txt

- Downloads all availiable pathways for the specified organism from KEGG.

- Creates pathway graphs from downloaded KGML files.

- Extracts linear subpathways from metabolic and non metabolic graphs.

- Extracts non linear subpathways from metabolic and non metabolic graphs.

- Downloads miRecords miRNA-mRNA interactions.

- Scores and evaluates (linear and non linear) subpathways to extract significant results.

- Organism identifier.

- Visualizes most the significant results ('.xlsx' or '.txt').

- Display informative messages (TRUE/FALSE).

- User-defined miRNA-mRNA interactions can be supplied in the form of an edgelist with two columns. If no such information is availiable, a missing or a NULL argument forces the use of default interactions by using `downloadMiRecords`.

### Value

.

### Examples

    # Default run

    load(system.file('extdata', 'Examples//data.RData', package='CHRONOS'))

    res <- CHRONOSrun(  mRNAexp=mRNAexpr,
                        mRNAlabel='entrezgene',
                        miRNAexp=miRNAexpr,
                        pathType=c('04915', '04917', '04930', '05031'),
                        org='hsa',
                        subType='Linear',
                        thresholds=c('subScore'=0.4, 'mirScore'=0.4),
                        miRNAinteractions=miRNAinteractions)

[Package CHRONOS version 1.16.0 Index]