R/bcepred_nmer.R

In mycobacrvR: Integrative Immunoinformatics for Mycobacterial Diseases in R Platform

bcepred_nmer = function (clas) 
{
  i1 = 1
  i2 = length(dir(pattern = ".RData"))
  for (i in i1:i2) {
    load(dir(pattern = ".RData")[i])
    temp = ls(pattern = clas)
    temp2 = lapply(temp, function(x) {
      tempm = get(x)
      lapply(tempm, function(x) {
        x@sequence
      })
    })
    org = NULL
    for (i in 1:length(temp)) {
      org = append(org, strsplit(temp[i], split = "_", 
                                 fixed = T)[[1]][1])
    }
    rv = which(org == "mtbh37rv")
    temp4 = NULL
    for (i in 1:length(temp2[[rv]])) {
      for (j in 1:length(temp2)) {
        temp4 = c(temp4, length(intersect(temp2[[j]], 
                                          temp2[[rv]][i])))
      }
    }
    temp5 = matrix(temp4, nrow = length(temp2[[rv]]), ncol = length(temp), 
                   byrow = T)
    colnames(temp5) = substr(temp, 1, 8)
    epitope_seq = as.matrix(temp2[[rv]], ncol = 1, byrow = T)
    gi_number = as.matrix(strsplit(temp[rv], split = "epitopes", 
                                   fixed = T)[[1]][2], ncol = 1, byrow = T)
    orthologs = as.matrix(length(temp) - 1, ncol = 1, byrow = T)
    epitope_length = NULL
    for (i in 1:length(get(temp[rv]))) {
      epitope_length = append(epitope_length, get(temp[rv])[[i]]@length)
    }
    class = as.matrix("bcepred", ncol = 1, byrow = T)
    conservation_ratio = NULL
    for (k in 1:nrow(temp5)) {
      conservation_ratio = append(conservation_ratio, 
                                  sum(temp5[k, 1:ncol(temp5)]) - 1)
    }
    temp6 = as.data.frame(temp5)
    temp6 = cbind(gi_number, orthologs, epitope_length, 
                  epitope_seq, conservation_ratio, class, temp6)
    colnames(temp6)[1:6] = c("ginumber", "Number_of_Orthologs", 
                             "Epitope_Length", "Epitope_Sequence", "Epitope_Conservation_Ratio", 
                             "Class")
    temp7 = temp6[1:nrow(temp6), 1:6]
    out <- data.frame(lapply(temp7, function(x) factor(unlist(x))))
    write.table(out, file = paste("bcepred_", strsplit(temp[rv], 
                                                       split = "epitopes", fixed = T)[[1]][2], ".txt", 
                                  sep = ""), sep = "\t", row.names = F)
    write.table(temp5, file = paste("bcepred_", strsplit(temp[rv], 
                                                         split = "epitopes", fixed = T)[[1]][2], "_metadata.txt", 
                                    sep = ""), sep = "\t", row.names = F)
    rm(list = ls()[!(ls() %in% c("clas"))])
  }
}