ssea.finish: Organize and save MSEA results
In zeynebkurtUCLA/Mergeomics: Integrative network analysis of omics data

Description Usage Arguments Details Value Author(s) References See Also Examples

ssea.finish organizes and stores the MSEA results into relevant output files.

1	ssea.finish(job)

job

data list including the results of MSEA process. job will be saved after getting organized:

label: unique identifier for the analysis.
folder: output folder for results.
resultsdata: frame including indexed module identities
(MODULE) and enrichment P-values (P).
database: database including indexed identities for 
modules, genes, and markers.

ssea.finish obtains module statistics (member genes, size, length, density, enrichment scores, false discovery rates), finds the top marker within genes, updates the gene scores and gene sizes (i.e. number of markers for each gene), and saves the organized results regarding the modules and genes into the relevant files.

job

data list including the organized results of MSEA process:

results: updated information of modules: 
number of distinct member genes (NGENES), 
number of distinct member markers (NLOCI), 
ratio of distinct to non-distinct markers (DENSITY), 
false discovery rates (FDR).
generesults: updated gene-specific information including:
indexed gene identity (GENE), 
gene size (NLOCI),
unadjusted enrichment score (SCORE), 
marker with maximum value (LOCUS), 
marker value (VALUE).

Ville-Petteri Makinen

Shu L, Zhao Y, Kurt Z, Byars SG, Tukiainen T, Kettunen J, Orozco LD, Pellegrini M, Lusis AJ, Ripatti S, Zhang B, Inouye M, Makinen V-P, Yang X. Mergeomics: multidimensional data integration to identify pathogenic perturbations to biological systems. BMC genomics. 2016;17(1):874.

ssea.analyze, ssea.control, ssea.prepare, ssea.start, ssea2kda

job.msea <- list()
job.msea$label <- "hdlc"
job.msea$folder <- "Results"
job.msea$genfile <- system.file("extdata", 
"genes.hdlc_040kb_ld70.human_eliminated.txt", package="Mergeomics")
job.msea$marfile <- system.file("extdata", 
"marker.hdlc_040kb_ld70.human_eliminated.txt", package="Mergeomics")
job.msea$modfile <- system.file("extdata", 
"modules.mousecoexpr.liver.human.txt", package="Mergeomics")
job.msea$inffile <- system.file("extdata", 
"coexpr.info.txt", package="Mergeomics")
job.msea$nperm <- 100 ## default value is 20000

## ssea.start() process takes long time while merging the genes sharing high
## amounts of markers (e.g. loci). it is performed with full module list in
## the vignettes. Here, we used a very subset of the module list (1st 10 mods
## from the original module file) and we collected the corresponding genes
## and markers belonging to these modules:
moddata <- tool.read(job.msea$modfile)
gendata <- tool.read(job.msea$genfile)
mardata <- tool.read(job.msea$marfile)
mod.names <- unique(moddata$MODULE)[1:min(length(unique(moddata$MODULE)),
10)]
moddata <- moddata[which(!is.na(match(moddata$MODULE, mod.names))),]
gendata <- gendata[which(!is.na(match(gendata$GENE, 
unique(moddata$GENE)))),]
mardata <- mardata[which(!is.na(match(mardata$MARKER, 
unique(gendata$MARKER)))),]

## save this to a temporary file and set its path as new job.msea$modfile:
tool.save(moddata, "subsetof.coexpr.modules.txt")
tool.save(gendata, "subsetof.genfile.txt")
tool.save(mardata, "subsetof.marfile.txt")
job.msea$modfile <- "subsetof.coexpr.modules.txt"
job.msea$genfile <- "subsetof.genfile.txt"
job.msea$marfile <- "subsetof.marfile.txt"
## run ssea.start() and prepare for this small set: (due to the huge runtime)
job.msea <- ssea.start(job.msea)
job.msea <- ssea.prepare(job.msea)
job.msea <- ssea.control(job.msea)
job.msea <- ssea.analyze(job.msea)
job.msea <- ssea.finish(job.msea)

## Remove the temporary files used for the test:
file.remove("subsetof.coexpr.modules.txt")
file.remove("subsetof.genfile.txt")
file.remove("subsetof.marfile.txt")