#' @title Counts some total information
#' @author Alexey Solovyev
#' @description Function counts sum of peaks, TFs and cellular lines for all IDs.
#'
#' @param dirFrom The path to output file. By default "~/tmp/RData/Output".
#'
#' @return Table of quantity of sum of peaks, TFs and cellular lines for all IDs.
#' In case of success it returns the word "Done".
#'
#' @usage makeSummarySeries(dirFrom="")
#'
#' @examples
#' makeSummarySeries(dirFrom="")
#'
#' @export
makeSummarySeries <- function(dirFrom="") {
if (dirFrom == "") {
dirFrom <- path.expand("~/tmp/RData/Output")
}
# dirTo <- dirFrom
arrayChrom <- gsub(pattern = ".RData", replacement = "", x = grep("^chr", list.files(dirFrom), value = TRUE))
# arrayChromTMP <- c("chr20", "chrY")
# genomeLen <- length(arrayChrom)
# arrayChrom <- arrayChromTMP
# minLim <- rep.int(x = 0, times = genomeLen)
# maxLim <- rep.int(x = 0, times = genomeLen)
# count <- rep.int(x = 0, times = genomeLen)
#
# annexe <- data.frame(Chromosome=arrayChrom, minLim, maxLim)
# row.names(annexe) <- arrayChrom
summarySeries <- data.frame()
summaryTmp <- data.frame()
# i <- arrayChrom[1]
ind_k <- 1
for (i in arrayChrom) {
message(i, ' from ', arrayChrom)
nameFileTest <- i
fileNameTest <- paste(nameFileTest, ".RData", sep = "")
dirTest <- dirFrom
myFileTest <- file.path(dirTest, fileNameTest)
frameTmp <- get(load(myFileTest))
rm(list = c("chr"))
listSeries <- unique(frameTmp$ID)
# j <- listSeries[1]
# totSer <- length(listSeries)
summaryTmp <- data.frame()
for (j in listSeries) {
# message(ind_k, ' from ', totSer)
frameTmpCalcule <- frameTmp[frameTmp$ID == j, ]
summaryTmp[ind_k, "Serie"] <- j
summaryTmp[ind_k, "Chromosome"] <- i
summaryTmp[ind_k, "Sum_Peaks"] <- nrow(frameTmpCalcule)
summaryTmp[ind_k, "TF_Unique"] <- length(unique(frameTmpCalcule$TF))
summaryTmp[ind_k, "Cell_Unique"] <- length(unique(frameTmpCalcule$Cell_Mod))
ind_k <- ind_k + 1
}
summarySeries <- rbind(summarySeries, summaryTmp)
}
fileNameOutput <- paste("summarySeries", ".RData", sep = "")
myFileOutput <- file.path(dirTest, fileNameOutput)
save(summarySeries, file=myFileOutput)
camelCaps <- "Done"
return(camelCaps)
}
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