R/F0003.R

In iCellR: Analyzing High-Throughput Single Cell Sequencing Data

#' Create an object of class iCellR.
#'
#' This function takes data frame and makes an object of class iCellR.
#' @param x A data frame containing gene counts for cells.
#' @return An object of class iCellR
#' @examples
#'      demo <- read.table(
#'      file = system.file('extdata', 'demo_data.txt', package = 'iCellR'),
#'      as.is = TRUE)
#'      myDemo.obj <- make.obj(demo)
#'      myDemo.obj
#' @export
make.obj <- function (x = NULL) {
  # get info
  INFO = "An object of class iCellR version:"
  INFO = paste(INFO, packageVersion("iCellR"))
  Data.Dim = dim(x)
  Data.Dim <- paste(Data.Dim , collapse=",")
  Data.Dim <- paste("Raw/original data dimentions (rows,columns):", Data.Dim)
  DATA <- colnames(x)
  Col.n <- head(DATA,3)
  Col.n <- paste(Col.n, collapse=",")
  Col.n <- paste("Columns names:" , Col.n, "...")
  Row.n <- head(row.names(x),3)
  Row.n <- paste(Row.n, collapse=",")
  Row.n <- paste("Row names:" , Row.n, "...")
  # get conditions
  do <- data.frame(do.call('rbind', strsplit(as.character(head(DATA,1)),'_',fixed=TRUE)))
  do <- dim(do)[2]
  if (do == 2) {
    My.Conds <- data.frame(do.call('rbind', strsplit(as.character(DATA),'_',fixed=TRUE)))[1]
    My.Conds <- as.data.frame(table(My.Conds))
    Conds <- paste(as.character(My.Conds$My.Conds) , collapse=",")
    cond.counts <- paste(as.character(My.Conds$Freq) , collapse=",")
    My.Conds <- paste("Data conditions in raw data: ", Conds, " (",cond.counts,")", sep="")
  } else {
    My.Conds = "Data conditions: no conditions/single sample"
  }
# paste
INFO.to.show <- paste(INFO, Data.Dim, My.Conds, Row.n, Col.n, sep="\n")
#INFO.to.show <- capture.output(message(INFO.to.show))
# make object
row.names(x) <- gsub("-",".",row.names(x))
colnames(x) <- gsub("-",".",colnames(x))
  object <- new(Class = "iCellR", obj.info = INFO.to.show, raw.data = x, data.conditions = My.Conds)
# return
  return(object)
}