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#' Append Survival Test Outputs
#'
#' Function used to append all .csv files that are outputted from AnalyzeOrthoMCL into one matrix.
#' @param work_dir the directory where the output files of AnalyzeOrthoMCL are located
#' @param out_name file name of outputted matrix
#' @param out_dir the directory where the outputted matrix is placed
#' @return A csv file containing a matrix with the following columns: OG, p-values, Bonferroni corrected p-values, mean phenotype of OG-containing taxa, mean pheotype of OG-lacking taxa, taxa included in OG, taxa not included in OG
#' @examples
#'
#' \dontrun{
#' file <- system.file('extdata', 'outputs', package='MAGNAMWAR')
#' directory <- paste(file, '/', sep = '')
#' SurvAppendMatrix(directory)
#' }
#'
#' @export
SurvAppendMatrix <- function(work_dir, out_name = "surv_matrix.csv",
out_dir = NULL) {
if (is.null(out_dir)) {
out_dir <- work_dir
}
orig_directory <- getwd()
if (getwd() != work_dir) {
setwd(work_dir)
}
filenames <- unlist(list.files(pattern = ".csv", full.names = F))
out_starve <- matrix(c(rep(1, 7)), ncol = 7)
for (i in filenames) {
data <- read.csv(paste(i, sep = ""), header = F)
if (grepl("Error", (data[1]))) {
break
} else {
for (k in 1:ncol(data)) {
final_data <- c(as.character(data[1, k]),
as.character(data[2, 1]),
as.character(data[3, 1]),
as.character(data[4, 1]),
as.character(data[5, 1]),
as.character(data[6, 1]),
as.character(data[7, 1]))
out_starve <- rbind(out_starve, final_data)
}
}
}
out_starve <- out_starve[-1, ]
row.names(out_starve) <- NULL
colnames(out_starve) <- c("OG", "p-val", "corrected_p-val",
"mean_OGContain", "mean_OGLack",
"taxa_contain", "taxa_miss")
write.csv(out_starve, out_name)
wd <- getwd()
cat(paste("Wrote:", out_name, "to", wd))
setwd(orig_directory)
}
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