md_exp: An example 'MinDistExperiment'

In rscharpf/MinimumDistance: A Package for De Novo CNV Detection in Case-Parent Trios

Description

This dataset contains log R ratios and B allele frequencies from a parent-offspring trio (three individuals). Only markers from chromosomes 7 and 22 are included in this object. The MinDistExperiment class extends RangedSummarizedExperiment, and so many of the methods defined for RangedSummarizedExperiment such as findOverlaps are available through inheritance.

Format

a MinDistExperiment

Examples

## Not run: 
    library(oligoClasses)
    library(VanillaICE)
    library(data.table)
    library(BSgenome.Hsapiens.UCSC.hg18)
    extdir <- system.file("extdata", package="VanillaICE")
    features <- suppressWarnings(fread(file.path(extdir, "SNP_info.csv")))
    fgr <- GRanges(paste0("chr", features$Chr), IRanges(features$Position, width=1),
                   isSnp=features[["Intensity Only"]]==0)
    fgr <- SnpGRanges(fgr)
    names(fgr) <- features[["Name"]]
    sl <- seqlevels(BSgenome.Hsapiens.UCSC.hg18)
    seqlevels(fgr) <- sl[sl %in% seqlevels(fgr)]
    seqinfo(fgr) <- seqinfo(BSgenome.Hsapiens.UCSC.hg18)[seqlevels(fgr),]
    fgr <- sort(fgr)
    files <- list.files(extdir, full.names=TRUE, recursive=TRUE, pattern="FinalReport")
    ## parse files
    parsedDir <- "ParsedFiles"
    if(!file.exists(parsedDir)) dir.create(parsedDir)
    views <- ArrayViews(rowRanges=fgr, sourcePaths=files, parsedPath=parsedDir)
    dat <- fread(files[1])
    select_columns <- match(c("SNP Name", "Allele1 - AB", "Allele2 - AB",
                              "Log R Ratio", "B Allele Freq"), names(dat))
    index_genome <- match(names(fgr), dat[["SNP Name"]])
    scan_params <- CopyNumScanParams(index_genome=index_genome, select=select_columns,
                                     cnvar="Log R Ratio",
                                     bafvar="B Allele Freq",
                                     gtvar=c("Allele1 - AB", "Allele2 - AB"))
    invisible(sapply(views, parseSourceFile, param=scan_params))
    ped_hapmap <- ParentOffspring(id = "hapmap", father="12287_03",
                                  mother="12287_02",
                                  offspring="12287_01",
                                  parsedPath=parsedPath(views))
    ped_list <- ParentOffspringList(pedigrees=list(
                                      ParentOffspring(id = "hapmap", father="12287_03",
                                                      mother="12287_02",
                                                      offspring="12287_01",
                                                      parsedPath=parsedPath(views)),
                                      ParentOffspring(id = "cleft",
                                                      father="22169_03",
                                                      mother="22169_02",
                                                      offspring="22169_01",
                                                      parsedPath=parsedPath(views))))
    sample_info <- read.csv(file.path(extdir, "sample_data.csv"), stringsAsFactors=FALSE)
    ind_id <- setNames(gsub(" ", "", sample_info$IndividualID), sample_info$File)
    colnames(views) <- ind_id[gsub(".csv", "", colnames(views))]
    md_exp <- MinDistExperiment(views, pedigree=ped_list[[2]])
    seqlevels(md_exp, pruning.mode="coarse") <- "chr22"
    params <- MinDistParam()
    md_gr <- segment2(md_exp, params)
    save(md_exp, file="~/Software/bridge/MinimumDistance/data/md_exp.rda")
    save(md_gr, file="~/Software/bridge/MinimumDistance/data/md_gr.rda")

## End(Not run)

rscharpf/MinimumDistance documentation built on Sept. 16, 2019, 4:12 a.m.