CHRONOS (version 1.0.3)

CHRONOSrun: 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.

Value

.

Details

• Imports gene and miRNA expressions from CHRONOS/extdata/Input/.txt and CHRONOS/extdata/Input/.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.

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)