MinimumDistance (version 1.16.0)

md_exp: 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, force=TRUE) <- "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)