Nothing
CHRONOSrun <- function(mRNAexp, mRNAlabel, miRNAexp, pathType, subType,
measures, thresholds, org, export, verbose,
miRNAinteractions)
{
if (missing(mRNAexp)) { mRNAexp <- 'mRNAexpressions.txt' }
if (missing(mRNAlabel)) { mRNAlabel <- 'entrezgene' }
if (missing(miRNAexp)) { miRNAexp <- 'miRNAexpressions.txt' }
if (missing(pathType)) { pathType <- 'All' }
if (missing(subType)) { subType <- 'All' }
if (missing(measures)) { measures <- 'FALSE' }
if (missing(org)) { org <- 'hsa' }
if (missing(export)) { export <- '.txt' }
if (missing(verbose)) { verbose <- FALSE }
if (missing(thresholds))
{
thresholds <- c('p-value'=0.04, 'subScore'=0.4, 'mirScore'=0.4)
}
if (missing(miRNAinteractions)) { miRNAinteractions <- NULL }
if (!verbose) { sink( tempfile() ) }
importExpressions(data=mRNAexp, type=mRNAlabel, sep='\t', org=org)
importExpressions(data=miRNAexp, org=org, type='miRNA', sep='\t')
# Download Insulin Signaling Pathway
paths <- downloadPathways(org=org, pathways=pathType)
# Create pathway graph
graphs <- createPathwayGraphs(org=org, pathways=paths)
if ( 'Linear' %in% subType || 'All' %in% subType )
{
# Extract linear subpathways
linSubs <- extractLinearSubpathways(graphs=graphs, filter=TRUE)
# Filter linear subpathways
linSubsScored <- scoreSubpathways(subpathways=linSubs,
filters=thresholds,
miRNAinteractions=miRNAinteractions)
if ( '.xlsx' %in% export )
{
to <- if (org == 'hsa') 'hgnc_symbol' else mRNAlabel
to <- if (org == 'mmu') 'mgi_symbol' else to
visualizeResults( summary=linSubsScored, export=export,
from=mRNAlabel, to=to )
}
}
if ( 'Non-Linear' %in% subType || 'All' %in% subType )
{
# Extract non linear subpathways
nliSubs <- extractNonLinearSubpathways(graphs=graphs, filter=TRUE)
# Filter non linear subpathways
nliSubsScored <- scoreSubpathways(subpathways=nliSubs,
filters=thresholds,
miRNAinteractions=miRNAinteractions)
if ( '.xlsx' %in% export )
{
to <- if (org == 'hsa') 'hgnc_symbol' else mRNAlabel
to <- if (org == 'mmu') 'mgi_symbol' else to
visualizeResults( summary=nliSubsScored, export=export,
from=mRNAlabel, to=to )
}
}
out <- list('graphs'=graphs)
if ( 'Linear' %in% subType )
{
out <- list('graphs'=graphs, 'linSubs'=linSubs,
'linSubsScored'=linSubsScored)
}
if ( 'Non-Linear' %in% subType )
{
out <- list('graphs'=graphs, 'nliSubs'=nliSubs,
'nliSubsScored'=nliSubsScored)
}
if ( 'All' %in% subType )
{
out <- list('graphs'=graphs, 'linSubs'=linSubs, 'nliSubs'=nliSubs,
'linSubsScored'=linSubsScored, 'nliSubsScored'=nliSubsScored)
}
if (!verbose) { sink() }
return(out)
}
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