R/methods-GRanges.R

In syounkin/Trioconductor: Trioconductor

setMethod("CNVMatrix",  signature(object="GRanges", gr="GRanges"), function(object, gr){ # sgy
  id.vec <- as.character(unique(names(object)))
  cmp.obj <- disjoin(object)
  cmp.gr <- disjoin(gr)
  cmp <- disjoin(c(cmp.obj,cmp.gr))
  cnv <- matrix(NA, nrow = length(id.vec), ncol = length(cmp) )
  for ( i in 1:length(id.vec) ){
    cnv[i,] <- countOverlaps( cmp, object[names(object) == id.vec[i]] )
  }
  rownames(cnv) <- id.vec
  colnames(cnv) <- paste0("comp",1:length(cmp))
  names(cmp) <- colnames(cnv)
  return(list(cnv.mat = cnv, cmp.gr = cmp, gr = object ))
})


setMethod("intersect2", signature(object="GRanges"), function( object ){
  disjoin(object)[countOverlaps(disjoin(object),object) == length(object)]
})