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#' Filter datasets according to no. features present in features with at least a certain depth.
#'
#' Filter the data based on the number of present features after filtering samples by depth of coverage.
#' There are many ways to filter the object, this is just one way.
#'
#' @param obj A MRexperiment object or count matrix.
#' @param present Features with at least 'present' postive samples.
#' @param depth Sampls with at least this much depth of coverage
#' @return A MRexperiment object.
#' @export
#' @examples
#'
#' data(mouseData)
#' filterData(mouseData)
#'
filterData <- function(obj,present=1,depth=1000){
mat = returnAppropriateObj(obj,norm=FALSE,log=FALSE)>0
cols = which(colSums(MRcounts(obj))>=depth)
rows = which(rowSums(mat[,cols])>=present)
return(obj[rows,cols])
}
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