#'Export Summary Count from Indel/SV Results
#'
#'@param Input Input file generated from MainSNVClass1,2.
#'
#'@param Mut_EL_th The threshold for mutant peptide to be neoantigen by EL.
#'
#'@param Mut_Rank_th The threshold for mutant peptide to be neoantigen by Rank.
#'
#'@param Total_RNA_th The total RNA expression threshold.
#'
#'@param Tumor_RNA_th The tumor specific RNA expression threshold.
#'
#'@param MutRatio_th The mutation ratio threshold.
#'
#'@param Weight The weight for alterations.
#'
#'@param WriteLongIndel If setting a file name, Write Long Indels of which the p-value is less than 0.05.
#'
#'@param IgnoreLongIndel Ignore Indels of which p-value is less than the indicated value for counting.
#'
#'@param DupCount Count for each different HLA type
#'
#'@return Num_Alteration The number of evaluated alterations.
#'
#'@return Num_Alteration_Generating_NeoAg The number of evaluated alterations that can generate neoantigen.
#'
#'@return Num_Peptide The number of evaluated peptifdes.
#'
#'@return Num_Peptide_Generating_NeoAg The number of evaluated peptides that can be neoantigen.
#'
#'@export
Export_Summary_IndelSV <- function(Input,
Mut_EL_th = NA,
Mut_Rank_th = NA,
Total_RNA_th = NA,
Tumor_RNA_th = NA,
MutRatio_th = NA,
Weight = NA,
WriteLongIndel = NA,
IgnoreLongIndel = 0,
DupCount = FALSE){
if((!is.na(Mut_EL_th) & !is.na(Mut_Rank_th)) | (is.na(Mut_EL_th) & is.na(Mut_Rank_th))){
print("Please Specify Either One of Mut_EL_th or Mut_Rank_th")
return(NULL)
}
# EL or Rank
m_th <- Mut_EL_th
m_th_column <- "Mut_EL"
if(!is.na(Mut_Rank_th)) {
m_th <- Mut_Rank_th
m_th_column <- "Mut_Rank"
}
# Attach Weight
if(!is.na(Weight[1])) {
Input <- cbind(Weight, Input)
colnames(Input)[1] <- "Weight"
}
# Calculate Pvalues
theoretical_pro <- 3 * 4^3 / 61^2
pvalues <- sapply(Input[, match("Mutant_Peptide", colnames(Input))], function(x) (1 - theoretical_pro)^nchar(x))
Input <- cbind(Input, pvalues)
colnames(Input)[ncol(Input)] <- "Pvalue"
index <- colnames(Input)
# Write Long Indels
if(!is.na(WriteLongIndel)){
unq <- unique(Input[, match("Mutant_Peptide", index)])
hit <- unq[as.numeric(Input[match(unq, Input[, match("Mutant_Peptide", index)]), match("Pvalue", index)]) < 0.001]
if(length(hit) > 0){
tmp <- Input[match(hit, Input[, match("Mutant_Peptide", index)]), (match("Chr", colnames(Input))):ncol(Input)]
if(length(hit)==1) tmp <- t(tmp)
write.table(tmp,
WriteLongIndel,
row.names = FALSE, col.names = FALSE, quote = FALSE, sep = "\t")
}
}
# Duplication
num_of_hla <- 1
if(DupCount){
Input[, match("Mutation_Position", index)] <- paste(Input[, match("HLA", index)], Input[, match("Mutation_Position", index)], sep = "_")
Input[, match("Evaluated_Mutant_Peptide", index)] <- paste(Input[, match("HLA", index)], Input[, match("Evaluated_Mutant_Peptide", index)], sep = "_")
num_of_hla <- length(unique(Input[, match("HLA", index)]))
}
# Count All
Num_Alteration <- length(unique(Input[, match("Mutation_Position", index)]))
Num_Peptide <- length(unique(Input[, match("Evaluated_Mutant_Peptide", index)]))
# Conditioning
if(IgnoreLongIndel > 0){
Input <- Input[pvalues > IgnoreLongIndel, ]
}
if(!is.na(Total_RNA_th)){
Input <- Input[as.numeric(Input[, match("Total_RNA", index)]) > Total_RNA_th, ]
}
if(!is.na(Tumor_RNA_th)){
Input <- Input[as.numeric(Input[, match("Tumor_RNA", index)]) > Tumor_RNA_th, ]
}
if(!is.na(MutRatio_th)){
Input <- Input[as.numeric(Input[, match("MutRatio", index)]) > MutRatio_th, ]
}
# Count Conditioned
Num_Cond_Alteration <- length(unique(Input[, match("Mutation_Position", index)]))
Num_Cond_Peptide <- length(unique(Input[, match("Evaluated_Mutant_Peptide", index)]))
# Extract by EL
Input <- Input[as.numeric(Input[, match(m_th_column, index)]) < m_th, ]
if(is.null(Input) | is.null(dim(Input)[1])) {
if(length(Input) > 10) {
Input <- t(Input)
}
}
# Count Rest
Num_Rest_Alteration <- length(unique(Input[, match("Mutation_Position", index)]))
Num_Rest_Peptide <- length(unique(Input[, match("Evaluated_Mutant_Peptide", index)]))
ans <- c(Num_Alteration / num_of_hla, Num_Cond_Alteration / num_of_hla, Num_Rest_Alteration / num_of_hla,
Num_Peptide / num_of_hla, Num_Cond_Peptide / num_of_hla, Num_Rest_Peptide / num_of_hla)
names(ans) <- c("Num_All_Alteration", "Num_Evaluated_Alteration", "Num_Alteration_Generating_NeoAg",
"Num_All_Peptide", "Num_Evaluated_Peptide", "Num_Peptide_Generating_NeoAg")
if(!is.na(Weight[1])){
alt_count <- sum(as.numeric(Input[match(unique(Input[, match("Mutation_Position", index)]),
Input[, match("Mutation_Position", index)]),
match("Weight", index)]))
pep_count <- sum(as.numeric(Input[match(unique(Input[, match("Evaluated_Mutant_Peptide", index)]),
Input[, match("Evaluated_Mutant_Peptide", index)]),
match("Weight", index)]))
ans <- c(ans[1:3], alt_count / num_of_hla, ans[4:6], pep_count / num_of_hla)
names(ans)[c(4, 8)] <- c("Weighted_Num_Alteration_Generating_NeoAg", "Weighted_Num_Peptide_Generating_NeoAg")
}
return(ans)
}
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