#' 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)
}
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