Bootstrap: Permanova Summarize Results

Define Libraries

library("stringr")
library("dplyr")
library("reshape2")
library("vegan")

Define Path

dir.wrk <- str_replace(getwd(), "/scripts", "")
dir.data <- file.path(dir.wrk, "data/data_permutation_withReplacement")
dir.output <- file.path(dir.wrk, "output")

Collect Permanova Results

nperm <- 1000

list.df <- list()
for (i in 1:nperm) {
    # DEFINE FILE ---
    file.dat <- file.path(dir.data, paste("stats_permanova_permmute_", i, ".tsv", 
        sep = ""))
    
    # LOAD DATA ---
    dat <- read.delim(file.dat, header = TRUE, stringsAsFactors = FALSE, row.names = 1)
    
    # RESHAPE DATA ---
    df <- reshape2::melt(as.matrix(dat))
    colnames(df) <- c("Feature", "Category", "Value")
    
    df$Feature <- as.character(df$Feature)
    df$Category <- as.character(df$Category)
    
    # STORE DATA ---
    list.df[[i]] <- df
}


### MERGE DATA ---
df <- do.call(cbind.data.frame, lapply(list.df, function(x) x[, 3]))
colnames(df) <- paste("Value", c(1:ncol(df)), sep = "_")

### AFFREGATE DATA ---
dm <- cbind(list.df[[1]][, 1:2], df)

# dm[,1:10]

### WRITE OUTPUT ---
file.output <- file.path(dir.output, "stats_anovatbl_permanova_permmute_results_withReplacement.tsv")
write.table(dm, file.output, sep = "\t", row.names = FALSE, col.names = TRUE, quote = FALSE)