R/modules_perfomed.R

In m-raheel/ShinyBeads: Interface for RnBeads generated reports

#' rnbi.analysis.modules.performed
#'
#' Takes in a working directory and returns a list of rnbeads modules performed
#' @param wd path to the rnbeads results directory where analysis.log file is located
#' @return list of rnbeads modules performed
#' @export


rnbi.analysis.modules.performed <- function(wd) {


  # if analysis log file is peresent than searching the file for the completed modules
  if ( file.exists( isolate({ paste(wd,'analysis.log',sep="/") }) ) ){

    resulting.modules.list <- list()
    module.counter <- 1

    check_vectors <- c('COMPLETED Loading Data', 'COMPLETED Quality Control', 'COMPLETED Preprocessing', 'COMPLETED Tracks and Tables','COMPLETED Covariate Inference','COMPLETED Exploratory Analysis','COMPLETED Differential Methylation')
    display_vectors <- c('Data Import', 'Quality Control', 'Preprocessing', 'Tracks and Tables','Covariate Inference','Exploratory Analysis','Differential Methylation')

    dat<- c('')
    logfile.path = reactive({file.path(wd, 'analysis.log')})
    A <- read.table(logfile.path(), sep="\t", fill=FALSE, strip.white=TRUE)
    dat <- data.frame(v=c(A))
    performed_modules <- 0
    count <- 0
    for (i in 1:length(check_vectors)) {

      result2 = with(dat, grepl(check_vectors[i], V1))

      for (j in 1:length(result2)) {

        if (result2[j] == TRUE){

          count <- count + 1

        }

      }

      if (count == 0) {

      }
      else{
        performed_modules <- i
        resulting.modules.list[module.counter] <- display_vectors[i]

        module.counter <- module.counter + 1

      }

      count <- 0
    }

    #print (resulting.modules.list)

    #session$sendCustomMessage(type = "myperformedmodulesno", performed_modules)

    return(resulting.modules.list)
  }

  else{

    empty.list <- list()


    return(empty.list)
  }

}


#' rnbi.analysis.rrbs.modules.performed
#'
#' Takes in a working directory and returns a list of rnbeads modules performed for RRBS analysis
#' @param wd path to the rnbeads results directory where index.html file is located
#' @return list of rnbeads modules performed
#' @export

rnbi.analysis.rrbs.modules.performed <- function(wd) {

  resulting.modules.list <- list()
  module.counter <- 1

  display_vectors <- c('Data Import', 'Quality Control', 'Preprocessing', 'Tracks and Tables','Covariate Inference','Exploratory Analysis','Differential Methylation')

  # if analysis log file is peresent than searching the file for the completed modules
  if ( file.exists( isolate({ paste(wd,'data_import.html',sep="/") }) ) ){

    resulting.modules.list[module.counter] <- display_vectors[1]
    module.counter <- module.counter + 1
  }

  if ( file.exists( isolate({ paste(wd,'quality_control.html',sep="/") }) ) ){

    resulting.modules.list[module.counter] <- display_vectors[2]
    module.counter <- module.counter + 1
  }

  if ( file.exists( isolate({ paste(wd,'preprocessing.html',sep="/") }) ) ){

    resulting.modules.list[module.counter] <- display_vectors[3]
    module.counter <- module.counter + 1
  }

  if ( file.exists( isolate({ paste(wd,'tracks_and_tables.html',sep="/") }) ) ){

    resulting.modules.list[module.counter] <- display_vectors[4]
    module.counter <- module.counter + 1
  }

  if ( file.exists( isolate({ paste(wd,'exploratory_analysis.html',sep="/") }) ) ){

    resulting.modules.list[module.counter] <- display_vectors[6]
    module.counter <- module.counter + 1
  }
  if ( file.exists( isolate({ paste(wd,'differential_methylation.html',sep="/") }) ) ){

    resulting.modules.list[module.counter] <- display_vectors[7]
    module.counter <- module.counter + 1
  }


  return(resulting.modules.list)

}