ssea.control {Mergeomics} | R Documentation

## Add internal positive control modules for MSEA

### Description

`ssea.control` adds positive control modules that includes the top-scored genes based on the marker scores of these genes. The database structure, including identities of the variables, is updated properly.

### Usage

    ssea.control(job)

### Arguments

`job` | data list including module and gene identities as characters; also including database that has indexed identities for MSEA:
    modules: module identities as characters.
    genes: gene identities as characters.
    moddata: preprocessed module data (indexed identities).
    database: database including indexed identities for
    modules, genes, and markers.

### Value

`job` | data list including augmented internal control modules:
    modules: augmented module names
    moddata: augmented module data
    database: augmented database

### Author(s)

Ville-Petteri Makinen

### References

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.

### Examples

    ## Check the slots for control module;
    ## if it cannot find any control module, function throws an error,
    ## if can find control slots, updates the database identities (modules,
    ## genes, markers) properly:
    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)

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

[Package Mergeomics version 1.20.0 Index]