R/slide.R

In 2eding/MTVR: R version of MultiTrans

#' slide
#'
#' slide function will execute SLIDE
#' see detail (http://slide.cs.ucla.edu/index.html)
#'
#' @param covBandMatrix is the SNP matrix, individual x SNPs
#' @param windowSize is the window size defined in terms of the number of SNPs.
#' @param numSampling is the number of sampling.
#' @param seedNum is set seed.
#' @param threshold is a text file containing pointwise p-values you want to correct, delimitered by space or newline.
#' @param outPath is a parameter that specifies the path of the result file
#' @param outName is a parameter that specifies the name of the result file
#'
#' @return kinship coefficient
#'
#' @examples
#'    X <- as.matrix(read.table(SNPData))
#'    K <- Kinship(X, outPath, outName)
#'    VC <- varComp(Y, K, numThreads, outPath, outName)
#'    corrMatrix <- generateR(X, K, VC, outPath, outName)
#'    covBandMatrix <- generateC(windowSize, corrMatrix, outPath = "./", outName = "c.txt")
#'
#'    result <- slide(covBandMatrix, windowSize, numSampling, seedNum, threshold, outPath, outName)
#' @export
#'
# 5. run slide (You can download slide from http://slide.cs.ucla.edu/)
# 5.1. slide_1prep
# ./slide.1.0/slide_1prep -C ./testData/c.txt 1000 ./testData/prep
# 5.2. slide_2run
# ./slide.1.0/slide_2run ./testData/prep ./testData/maxstat 100 123
# 5.3. slide_3sort
# ./slide.1.0/slide_3sort ./testData/sorted ./testData/maxstat
# 5.4. slide_4correct
# ./slide.1.0/slide_4correct -p ./testData/sorted threshold.txt ./testData/MultiTrans.output

slide <- function(covBandMatrix, windowSize, numSampling, seedNum, threshold, outPath, outName){
  step1 <- system.file('./slide_1prep', package='MTVR')
  Sys.chmod(step1)
  slide_step1 <- function(covBandMatrix, windowSize, outPath){
    system(paste(step1, "-C", covBandMatrix, windowSize, outPath, "prep", sep = ""))
    step1_prep <- as.matrix(data.table::fread(paste(outPath, "prep", sep = "")))
  }

  step2 <- system.file('./slide_2run', package='MTVR')
  Sys.chmod(step2)
  slide_step2 <- function(step1_prep, outPath, numSampling, seedNum){
    system(paste(step2, step1_prep, outPath, "maxstat", numSampling, seedNum, sep = ""))
    step2_prep <- as.matrix(data.table::fread(paste(outPath, "maxstat", sep = "")))
  }

  step3 <- system.file('./slide_3sort', package='MTVR')
  Sys.chmod(step3)
  slide_step3 <- function(outPath, step2_prep){
    system(paste(step3, outPath, "sorted", step2_prep))
    step3_prep <- as.matrix(data.table::fread(paste(outPath, "sorted", sep = "")))
  }

  step4 <- system.file('./slide_4correct', package='MTVR')
  Sys.chmod(step4)
  slide_step4 <- function(step3_prep, threshold, outPath, outName){
    system(paste(step4, "-p", step3_prep, threshold, outPath, outName, sep = ""))
    result <- as.matrix(data.table::fread(paste(outPath, outName, sep = "")))
  }

  return(result)
}