#' @title Search by address
#' @author Alexey Solovyev
#' @description Function selects in given address.
#'
#' @param dirFrom Path to data, by default "~/tmp/RData/Output".
#' @param nameChromosome Name of chromosome.
#' @param begin Position of starting of searching on chromosome.
#' @param end Position of ending of searching on chromosome.
#' @param firstCut Can be "in" or "out". Condition of searching. "in" means that begin of MACS-peak can be before param "begin".
#' "out" means that begin of MACS-peak can be only after param "begin".
#' @param secondCut Can be "in" or "out". Condition of searching. "in" means that end of MACS-peak can be after param "end".
#' "out" means that end of MACS-peak can be only before param "end".
#'
#' @return Data Frame (class = "data.frame") of peaks in this address.
#'
#' @usage fetchCoordsFiles(dirFrom = "", nameChromosome = "chr21", begin = "", end = "",
#' firstCut = "in", secondCut = "in")
#'
#' @examples
#' myFrame <- fetchCoordsFiles(dirFrom = "", nameChromosome = "chr21", begin = "",
#' end = "", firstCut = "in", secondCut = "in")
#'
#' @export
fetchCoordsFiles <- function(dirFrom = "",
nameChromosome = "chr21",
begin = "",
end = "",
firstCut = "in",
secondCut = "in") {
annexe <- data.frame()
if (!(firstCut %in% c("in", "out"))|!(secondCut %in% c("in", "out"))) {
message("Choose 'firstCut' and 'secondCut' from the following: ", paste( c("'in'", "'out'"), collapse=" "))
stop()
}
if (dirFrom == "") {
dirFrom <- path.expand("~/tmp/RData/Output")
}
fileNameAnnexe <- paste(dirFrom, "/annexe.RData", sep = "")
load(fileNameAnnexe)
if (class(begin) == "character") {
begin <- annexe[annexe$Chromosome == nameChromosome, "minLim"]
}
if (class(end) == "character") {
end <- annexe[annexe$Chromosome == nameChromosome, "maxLim"]
}
if (begin > end) {
message("The 'begin' must be less than the 'end'.")
stop()
}
if (nameChromosome == ""|(!(nameChromosome %in% annexe$Chromosome))) {
listChr <- paste(annexe$Chromosome, collapse=" ")
message("Choose from the following chromosomes: ", listChr)
stop()
}
myFileOpen <- file.path(dirFrom, paste(nameChromosome, ".RData", sep = ""))
frameTmp <- get(load(myFileOpen))
rm(list = c("chr"))
if ((firstCut == "in") & (secondCut == "in")) {
frameRep <- frameTmp[which(frameTmp$Begin <= end & frameTmp$End >= begin), ]
}
if ((firstCut == "out") & (secondCut == "out")) {
frameRep <- frameTmp[which(frameTmp$Begin >= begin & frameTmp$End <= end), ]
}
if ((firstCut == "in") & (secondCut == "out")) {
frameRep <- frameTmp[which(frameTmp$End >= begin & frameTmp$End <= end), ]
}
if ((firstCut == "out") & (secondCut == "in")) {
frameRep <- frameTmp[which(frameTmp$Begin >= begin & frameTmp$Begin <= end), ]
}
return(frameRep)
}
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