ssea.start.relabel {Mergeomics} | R Documentation

## Update gene symbols after merging overlapped markers

### Description

`ssea.start.relabel` updates gene symbols within the modules after merging overlapping genes that contain shared markers

### Usage

    ssea.start.relabel(dat, grp)

### Arguments

`dat` | module data corresponding gene sets
`grp` | gene data that is needed to be relabeled after the merging process of the overlapping markers

### Value

`dat` | relabeled module data of `grp`

### 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)

    ## Import moddata:
    moddata <- tool.read(job.msea$modfile, c("MODULE", "GENE"))
    moddata <- unique(na.omit(moddata))

    ## Import marker (e.g. locus) values:
    locdata <- tool.read(job.msea$locfile, c("LOCUS", "VALUE"))
    locdata$VALUE <- as.double(locdata$VALUE)
    rows <- which(0*(locdata$VALUE) == 0)
    locdata <- unique(na.omit(locdata[rows,]))
    locdata_ex <- locdata
    names(locdata_ex) <- c("MARKER","VALUE")
    ## Import mapping data between genes and markers:
    gendata <- tool.read(job.msea$genfile, c("GENE", "LOCUS"))
    gendata <- unique(na.omit(gendata))
    gendata_ex <- gendata
    names(gendata_ex) <- c("GENE","MARKER")

    ## Remove genes with no marker values:
    pos <- match(gendata$LOCUS, locdata$LOCUS)
    gendata <- gendata[which(pos > 0),]

    ## Merge overlapping genes:
    gendata <- tool.coalesce(items=gendata$LOCUS, groups=gendata$GENE,
    rcutoff=job.msea$maxoverlap)
    job.msea$geneclusters <- gendata[,c("CLUSTER","GROUPS")]
    job.msea$geneclusters <- unique(job.msea$geneclusters)

    ## Update gene symbols after merging the overlapping ones:
    moddata <- ssea.start.relabel(moddata, gendata)
    gendata <- unique(gendata[,c("GROUPS", "ITEM")])
    names(gendata) <- c("GENE", "LOCUS")

    ## 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 1.10.0 Index]