md_exp {MinimumDistance} | R Documentation

## An example `MinDistExperiment`

### 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)

[Package MinimumDistance version 1.36.0 Index]