TCGA.pipe {ELMER} | R Documentation

## ELMER analysis pipeline for TCGA data.

### Description

ELMER analysis pipeline for TCGA data. This pipeline combine every steps of ELMER analyses: get.feature.probe, get.diff.meth, get.pair, get.permu, get.enriched.motif and get.TFs. Every steps' results are saved.

### Usage

    TCGA.pipe(disease, genome = "hg38", analysis = "all", wd = getwd(),
      cores = 1, mode = "unsupervised", Data = NULL, diff.dir = "hypo",
      genes = NULL, mutant_variant_classification = c("Frame_Shift_Del",
      "Frame_Shift_Ins", "Missense_Mutation", "Nonsense_Mutation",
      "Splice_Site", "In_Frame_Del", "In_Frame_Ins", "Translation_Start_Site",
      "Nonstop_Mutation"), group.col = "TN", group1 = "Tumor",
      group2 = "Normal", ...)

### Arguments

`disease` | TCGA short form disease name such as COAD
`genome` | Data aligned against which genome of reference. Options: "hg19", "hg38" (default)
`analysis` | A vector of characters listing the analysis need to be done. Analysis can be "download","distal.probes","diffMeth","pair","motif","TF.search". Default is "all" meaning all the analysis will be processed.
`wd` | A path shows working dirctory. Default is "./"
`cores` | A interger which defines number of core to be used in parallel process. Default is 1: don't use parallel process.
`mode` | This option will automatically set the percentage of samples to be used in the analysis. Options: "supervised" (use 100% of samples) or "unsupervised" (use 20% of samples).
`Data` | A path shows the folder containing DNA methylation, expression and clinic data
`diff.dir` | A character can be "hypo" or "hyper", showing dirction DNA methylation changes. If it is "hypo", get.diff.meth function will identify all significantly hypomethylated CpG sites; If "hyper", get.diff.meth function will identify all significantly hypermethylated CpG sites
`genes` | List of genes for which mutations will be verified. A column in the MAE with the name of the gene will be created with two groups WT (tumor samples without mutation), MUT (tumor samples w/ mutation), NA (not tumor samples)
`mutant_variant_classification` | List of TCGA variant classification from MAF files to consider a samples mutant. Only used when argument gene is set.
`group.col` | A column defining the groups of the sample. You can view the available columns using: colnames(MultiAssayExperiment::colData(data)).
`group1` | A group from group.col. ELMER will run group1 vs group2. That means, if direction is hyper, get probes hypermethylated in group 1 compared to group 2.
`group2` | A group from group.col. ELMER will run group1 vs group2. That means, if direction is hyper, get probes hypermethylated in group 1 compared to group 2.
`...` | A list of parameters for functions: GetNearGenes, get.feature.probe, get.diff.meth, get.pair

### Value

Different analysis results.

### Examples

      data <- ELMER:::getdata("elmer.data.example")
      TCGA.pipe(disease = "LUSC",
                data = data,
                analysis = c("diffMeth","pair", "motif","TF.search"),
                mode = "supervised",
                group.col = "definition",
                group1 = "Primary solid Tumor",
                group2 = "Solid Tissue Normal",
                diff.dir = c("hypo"),
                dir.out = "pipe",
                sig.dif = 0.0001,
                pvalue = 1.0,
                min.incidence = 0,
                lower.OR = 0.0)
    ## Not run:
      distal.probe <- TCGA.pipe(disease = "LUSC", analysis="distal.enhancer", wd="~/")
      TCGA.pipe(disease = "LUSC",analysis = "all", genome = "hg19", cores = 1, permu.size=300, Pe=0.01)
      projects <- TCGAbiolinks:::getGDCprojects()$project_id
      projects <- gsub("TCGA-","",projects[grepl('^TCGA',projects,perl=TRUE)])
      for(proj in projects) TCGA.pipe(disease = proj,analysis = "download")
      plyr::alply(sort(projects),1,function(proj) {
           tryCatch({
             print(proj);
             TCGA.pipe(disease = proj,analysis = c("createMAE"))})
           }, .progress = "text")
      plyr::alply(sort(projects),1,function(proj) {
        tryCatch({
          print(proj);
          TCGA.pipe(disease = proj,
                     analysis = c("diffMeth","pair", "motif","TF.search"))})
      }, .progress = "text")

      # Evaluation mutation
      TCGA.pipe(disease = "LUSC",analysis = "createMAE",gene = "NFE2L2")
      TCGA.pipe(disease = "LUSC",analysis = c("diffMeth","pair", "motif","TF.search"),
                mode = "supervised",
                group.col = "NFE2L2", group1 = "Mutant", group2 = "WT",
                diff.dir = c("hypo"),
                dir.out = "LUSC_NFE2L2_MutvsWT")

    ## End(Not run)

[Package ELMER version 2.8.3 Index]