TCGA.pipe: ELMER analysis pipeline for TCGA data.

In ELMER: Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

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)

ELMER documentation built on Nov. 8, 2020, 4:59 p.m.