R/methods-FileViews.R

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

##FileViews <- function(path=character(), pedigree=list(),
##                      cnvar=character(), bafvar=character(),
##                      fid=character(),
##                      importfun=function(){},
##                      annot_pkg=character()){
##  new("FileViews", path=path, pedigree=pedigree, cnvar=cnvar, bafvar=bafvar,
##      fid=fid, importfun=importfun, annot_pkg=character())
##}
##
##.path <- function(object) object@path
##filenames <- function(object) as.character(pedigree(object)[[1]])
##
##setMethod("nrow", "FileViews", function(x) length(x@pedigree))
##setMethod("length", "FileViews", function(x) length(x@pedigree))
##setMethod("pedigree", "FileViews", function(object) object@pedigree)
##cnvar <- function(object) object@cnvar
##bafvar <- function(object) object@bafvar
##fid <- function(object) object@fid
##
##setMethod("show", "FileViews", function(object){
##  cat("class 'FileViews'\n")
##  cat("   No. pedigrees:", length(object), "\n")
##  cat("   path to RDS files:", .path(object), "\n")
##})
##
##setMethod("[", "FileViews", function(x, i, j, ..., drop=FALSE){
##  if(!missing(i)){
##    x@pedigree <- pedigree(x)[i]
##  }
##  x
##})

##pednames <- function(object) names(pedigree(object)[[1]])

##setMethod("assays", "FileViews", function(x, ...){
##  if(nrow(x) > 1) stop("object contains several trios. Use [i, ] to subset the ith trio prior to calling assays")
##  files <- file.path(.path(x), filenames(x))
##  tmp <- lapply(files, x@importfun)
##  tmp <- lapply(tmp, as.data.frame)
##  cnindex <- grep(cnvar(x), colnames(tmp[[1]]))
##  bindex <- grep(bafvar(x), colnames(tmp[[1]]))
##  if(length(cnindex) != 1) stop("cnvar not correctly specified")
##  if(length(bindex) != 1) stop("bafvar not correctly specified")
##  lrrlist <- lapply(tmp, "[", cnindex)
##  baflist <- lapply(tmp, "[", bindex)
##  r <- setNames(do.call(cbind, lrrlist), pednames(x))
##  b <- setNames(do.call(cbind, baflist), pednames(x))
##  r <- as.matrix(r)
##  b <- as.matrix(b)
##  if(fid(x) != ""){
##    findex <- grep(fid(x), colnames(tmp[[1]]))
##    fid <- tmp[[1]][, findex]
##    rownames(r) <- rownames(b) <- fid
##  }
##  snpArrayAssays(cn=r, baf=b)
##})

##setGeneric("files", function(object) standardGeneric("files"))
##setMethod("FileViews", "FileViews", function(object){
##  file.path
##})


##setMethod(MAP2, "FileViews", function(object, mdgr, param, rowRanges, ...){
##  object <- object[1]
##  assayList <- assays(object)
##  ped <- pedigree(object)
##  me <- MinDistExperiment(assays=assayList,
##                          rowRanges=rowRanges,
##                          colData=setNames(DataFrame(ped), "filename"))
##  me <- subsetAndSort(me, seqlevels(me)[1:22])
##  mdgr <- segment2(me, param=param)
##  mindist(mdgr) <- narrow2(mdgr, param)
##  mindist(mdgr) <- MAP2(me, mdgr, param)
##})

##FileViews <- function(path=character(), pedigree=list(),
##                      cnvar=character(), bafvar=character(),
##                      fid=character(),
##                      importfun=function(){},
##                      annot_pkg=character()){
##  new("FileViews", path=path, pedigree=pedigree, cnvar=cnvar, bafvar=bafvar,
##      fid=fid, importfun=importfun, annot_pkg=character())
##}

##.path <- function(object) object@path
##filenames <- function(object)
##
##setMethod("nrow", "FileViews", function(x) length(x@pedigree))
##setMethod("length", "FileViews", function(x) length(x@pedigree))
##setMethod("pedigree", "FileViews", function(object) object@pedigree)
##cnvar <- function(object) object@cnvar
##bafvar <- function(object) object@bafvar
##fid <- function(object) object@fid
##
##setMethod("show", "FileViews", function(object){
##  cat("class 'FileViews'\n")
##  cat("   No. pedigrees:", length(object), "\n")
##  cat("   path to RDS files:", .path(object), "\n")
##})
##
##setMethod("[", "FileViews", function(x, i, j, ..., drop=FALSE){
##  if(!missing(i)){
##    x@pedigree <- pedigree(x)[i]
##  }
##  x
##})