R/segData-accessors.R

In segmentSeq: Methods for identifying small RNA loci from high-throughput sequencing data

# modification on git from copied files
#setMethod("[", "segData", function(x, i, j, ..., drop = FALSE) {
#  x <- callNextMethod(x, i, j, ..., drop = FALSE)
#  if(!missing(i))
#    {
#      i <- as.vector(i)
#      if(nrow(x@data) > 0) x@data <- x@data[i,, drop = FALSE]
#    }
#
#  if(!missing(j))
#    {
#      j <- as.vector(j)
#      x@data <- x@data[,j,drop = FALSE]
#      x@libsizes <- x@libsizes[j]
#    }  
#  x
#})

#setMethod("dim", "segData", function(x) {
#  c(max(length(x@coordinates), nrow(x@data)), length(x@replicates))
#})


#setValidity("segData", function(object) {
#  validmess <- c()
#  valid <- TRUE
#  if(length(object@libsizes) != ncol(object))
#    {
#      valid <- FALSE
#      validmess <- c(validmess, "Length of '@libsizes' slot must equal length of '@replicates' slot.")
#    }
#  if(nrow(object@data) != length(object@coordinates) & nrow(object@data) != 0 & length(object@coordinates) != 0)
#    {
#      valid <- FALSE
#      validmess <- c(validmess, "Number of rows of '@data' slot (if not zero) must be the same as '@coordinates' slot (if not zero).")
#    }
#  if(ncol(object@data) > 0 && !all(as.integer(object@data) == object@data))
#    {
#      valid <- FALSE
#      validmess <- c(validmess, "All members of the '@data' matrix must be castable as integers.")
#    }
#  if(ncol(object@data) != length(object@replicates) & ncol(object@data) != 0 & length(object@replicates) != 0)
#    {
#      valid <- FALSE
#      validmess <- c(validmess, "Number of columns of '@data' slot (if not zero) must be the same as the length of the '@replicates' slot (if not zero).")
#    }
#  if(valid) return(valid) else validmess
#})


#setMethod("show", "segData", function(object) {
#  callNextMethod(object)
#  cat('\nSlot "data":\n')
#  cat("Matrix with ", nrow(object@data), " rows.")
#  .printIRangesMatrix(object@data)
#  cat('\nSlot "libsizes":\n')
#  print(object@libsizes)
#})