md_exp {MinimumDistance} | R Documentation |
MinDistExperiment
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.
a MinDistExperiment
## 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)