CHRONOSrun: Default run of CHRONOS

In CHRONOS: CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis

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)

CHRONOS documentation built on Nov. 8, 2020, 8:30 p.m.