R/stripMethyLumiSet.R

In methylumi: Handle Illumina methylation data

## FIXME: the real answer is to farm the data out to ff or hdf5, like Benilton
stripBeadNs <- function(object) { # {{{ make 450k datasets smaller
  if( 'methylated.N' %in% assayDataElementNames(object) ||
      'unmethylated.N' %in% assayDataElementNames(object) ) { 
    history.submitted <- as.character(Sys.time())
    aData <- assayData(object)
    storageMode(aData) <- "environment"
    rm('unmethylated.N', envir=aData)
    rm('methylated.N', envir=aData)
    storageMode(aData) <- "lockedEnvironment"
    assayData(object) <- aData
    history.finished <- as.character(Sys.time())
    history.command <- deparse(match.call())
    oldHistory <- object@history
    newHistory <- data.frame(submitted=history.submitted, 
                             finished=history.finished,
                             command=history.command)
    if(is(object, 'MethyLumiM')) newHistory$lumiVersion = NA
    object@history<- rbind(oldHistory, newHistory)
  }
  return(object)
} # }}}
stripBeadSDs <- function(object) { # {{{
  if( 'methylated.SD' %in% assayDataElementNames(object) ||
      'unmethylated.SD' %in% assayDataElementNames(object) ) { 
    history.submitted <- as.character(Sys.time())
    aData <- assayData(object)
    storageMode(aData) <- "environment"
    rm('unmethylated.SD', envir=aData)
    rm('methylated.SD', envir=aData)
    storageMode(aData) <- "lockedEnvironment"
    assayData(object) <- aData
    history.finished <- as.character(Sys.time())
    history.command <- deparse(match.call())
    oldHistory <- object@history
    newHistory <- data.frame(submitted=history.submitted, 
                             finished=history.finished,
                             command=history.command)
    if(is(object, 'MethyLumiM')) newHistory$lumiVersion = NA
    object@history<- rbind(oldHistory, newHistory)
  }
  return(object)
} # }}} 
stripOOB <- function(object) { # {{{
  if( 'methylated.OOB' %in% assayDataElementNames(object) ||
      'unmethylated.OOB' %in% assayDataElementNames(object) ) { 
    history.submitted <- as.character(Sys.time())
    aData <- assayData(object)
    storageMode(aData) <- "environment"
    rm('unmethylated.OOB', envir=aData)
    rm('methylated.OOB', envir=aData)
    storageMode(aData) <- "lockedEnvironment"
    assayData(object) <- aData
    history.finished <- as.character(Sys.time())
    history.command <- deparse(match.call())
    oldHistory <- object@history
    newHistory <- data.frame(submitted=history.submitted, 
                             finished=history.finished,
                             command=history.command)
    if(is(object, 'MethyLumiM')) newHistory$lumiVersion = NA
    object@history<- rbind(oldHistory, newHistory)
  }
  return(object)
} # }}}
stripMethyLumiSet <- function(object) { # {{{
  return(stripOOB(stripBeadSDs(stripBeadNs(object))))
} # }}}