R/normFuncs.R

In synlet: Hits Selection for Synthetic Lethal RNAi Screen Data

#' @import magrittr
#' @import ggplot2
#' @importFrom dplyr filter
#' @importFrom reshape2 dcast
#' @importFrom doBy summaryBy
#' @keywords internal
.ff_plateNorm <- function(masterPlate, dat) {
  # browser()
  masterp.da <- dplyr::filter(dat, MASTER_PLATE == masterPlate, 
    EXPERIMENT_TYPE == "sample", WELL_CONTENT_NAME != "empty")
  masterp.da$PLATE <- as.character(masterp.da$PLATE)
  tem.1 <- doBy::summaryBy(READOUT ~ PLATE, data = masterp.da, 
    FUN = median, na.rm = TRUE)
  colnames(tem.1)[2] <- "PLATE_MED"
  masterp.da.1 <- merge(masterp.da, tem.1, by.x = "PLATE", by.y = "PLATE")
  tem.2 <- masterp.da.1$READOUT / masterp.da.1$PLATE_MED
  masterp.da.1 <- data.frame(masterp.da.1, NORMEDV = tem.2)
  # masterp.da.1
}

#' @keywords internal
.ff_contsiRNANorm <- function(masterPlate, dat, contsiRNA) {
  # browser()
  masterp.da <- dplyr::filter(dat, MASTER_PLATE == masterPlate, 
    EXPERIMENT_TYPE == "sample", WELL_CONTENT_NAME != "empty")
  control.da <- dplyr::filter(dat, MASTER_PLATE == masterPlate,
    WELL_CONTENT_NAME == contsiRNA)

  masterp.da$PLATE <- as.character(masterp.da$PLATE)
  control.da$PLATE <- as.character(control.da$PLATE)
  tem.1 <- doBy::summaryBy(READOUT ~ PLATE, data = control.da, FUN = median, na.rm = TRUE)
  # if (! all(complete.cases(tem.1))) browser()
  colnames(tem.1)[2] <- "CONTROL_MED"
  ## contain all masterplate data, even in the condition no control available.
  masterp.da.1 <- merge(masterp.da, tem.1, by.x = "PLATE", by.y = "PLATE", all.x = TRUE)
  ## normalize to the median.
  tem.2 <- masterp.da.1$READOUT / masterp.da.1$CONTROL_MED
  masterp.da.1 <- cbind(masterp.da.1, NORMEDV = tem.2)
  # masterp.da.1
}

#' @keywords internal
.ff_masterPlateValue <- function(masterPlate, dat, treatment,
  control, normMethod = "PLATE") {
  if (normMethod == "PLATE") {
    masterp.da.1 <- .ff_plateNorm(masterPlate, dat)
  } else {
    masterp.da.1 <- .ff_contsiRNANorm(masterPlate, dat, normMethod)
  }

  treat.p <- dplyr::filter(masterp.da.1, EXPERIMENT_MODIFICATION == treatment) %>%
    extract2("PLATE") %>%
    as.character %>%
    unique

  cont.p <- dplyr::filter(masterp.da.1, EXPERIMENT_MODIFICATION == control) %>%
    extract2("PLATE") %>%
    as.character %>%
    unique

  # browser()
  if (length(treat.p) != 0 & length(cont.p) != 0) {
    ## treatment first, followed by controls;
    plate.paired <- c(treat.p, cont.p)
    masterp.da.2 <- reshape2::dcast(masterp.da.1, WELL_CONTENT_NAME ~ PLATE,
      value.var = "NORMEDV")
    rownames(masterp.da.2) <- masterp.da.2$WELL_CONTENT_NAME
    masterp.da.2 <- as.data.frame(masterp.da.2[, -1])
    masterp.da.2 <- masterp.da.2[, plate.paired]
    master.norm <- list(normedV = masterp.da.2, treat.num = length(treat.p),
      cont.num = length(cont.p))
    # master.norm

  } else {
    stop("--- Empty control or treament plates in master plate:", 
      masterPlate, "---\n")
  }
}