Nothing
iedb_consensus_mhcii_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@comblib_core
})
})
org = NULL
for (j in 1:length(temp)) {
org = append(org, strsplit(temp[j], split = "_",
fixed = T)[[1]][1])
}
rv = which(org == "mtbh37rv")
temp4 = NULL
for (k in 1:length(temp2[[rv]])) {
for (l in 1:length(temp2)) {
temp4 = c(temp4, length(intersect(temp2[[l]],
temp2[[rv]][k])))
}
}
temp5 = matrix(temp4, nrow = length(temp2[[rv]]), ncol = length(temp),
byrow = T)
check1 = strsplit(temp, "_", fixed = TRUE)
check2 = unlist(lapply(check1, function(x) {
return(x[1])
}))
colnames(temp5) = check2
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]]@epitope_length)
}
class = as.matrix("iedb_consensus_mhcii", ncol = 1,
byrow = T)
allele = unlist(lapply(get(temp[rv]), function(x) {
x@Allele
}))
conservation_ratio = NULL
for (m in 1:nrow(temp5)) {
conservation_ratio = append(conservation_ratio,
sum(temp5[m, 1:ncol(temp5)]) - 1)
}
checka = unlist(lapply(get(temp[rv]), function(x) {
x@comblib_score
}))
temp6 = as.data.frame(temp5)
temp6 = cbind(gi_number, checka, allele, orthologs,
epitope_length, epitope_seq, conservation_ratio,
class, temp6)
colnames(temp6)[1:8] = c("ginumber", "score", "Allele",
"Number_of_Orthologs", "Epitope_Length", "Epitope_Sequence",
"Epitope_Conservation_Ratio", "class")
temp7 = temp6[1:nrow(temp6), 1:8]
out <- data.frame(lapply(temp7, function(x) factor(unlist(x))))
metadata = cbind(as.character(out$ginumber), as.character(out$Allele),
as.character(out$score), as.character(out$Epitope_Sequence),
as.character(out$class), temp5)
colnames(metadata)[1:5] = c("ginumber", "Allele", "score",
"Epitope_Sequence", "class")
write.table(out, file = paste("iedb_consensus_mhcii_",
strsplit(temp[rv], split = "epitopes", fixed = T)[[1]][2],
".txt", sep = ""), sep = "\t", row.names = F)
write.table(metadata, file = paste("iedb_consensus_mhcii_",
strsplit(temp[rv], split = "epitopes", fixed = T)[[1]][2],
"_metadata.txt", sep = ""), sep = "\t", row.names = F)
rm(list = ls()[!(ls() %in% c("clas"))])
}
}
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