ssea.start.configure {Mergeomics} | R Documentation

## Check parameters before MSEA

### Description

`ssea.start.configure` checks the input parameter before MSEA process starts and assigns default values for non-exist fields of the input data object.

### Usage

    ssea.start.configure(plan)

### Arguments

`plan` | a data list with the following components:
    label: unique identifier for the analysis
    folder: output folder for results
    modfile: path to module file (cols: MODULE GENE)
    marfile: path to marker file (cols: MARKER VALUE)
    genfile: path to gene file (cols: GENE MARKER)
    inffile: path to module info file (cols: MODULE DESCR)
    seed: seed for random number generator
    permtype: gene for gene-level, marker for marker-level
    nperm: max number of random permutations
    mingenes: min number of genes per module (after merging)
    maxgenes: max number of genes per module
    quantiles: cutoffs for test statistic
    maxoverlap: max overlap allowed between genes

### Value

`plan` | a data list including checked and assigned values (to non-existing fields) of the input parameter:
    label: unique identifier for the analysis
    folder: output folder for results
    modfile: path to module file (cols: MODULE GENE)
    marfile: path to marker file (cols: MARKER VALUE)
    genfile: path to gene file (cols: GENE MARKER)
    inffile: path to module info file (cols: MODULE DESCR)
    seed: seed for random number generator
    permtype: gene for gene-level, marker for marker-level
    nperm: max number of random permutations
    mingenes: min number of genes per module (after merging)
    maxgenes: max number of genes per module
    quantiles: cutoffs for test statistic
    maxoverlap: max overlap allowed between genes

### 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.

### See Also

`ssea.start`

### Examples

    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() for this small set:(due to the huge runtime we did not use
    ## full sets of modules, genes, and markers)
    job.msea <- ssea.start.configure(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]