MainSeqFragmentClass2: Calculate Neoantigen Candidates from A Given Sequence for MHC...

In hase62/Neoantimon: Neoantimon: A multifunctional R package for identification of tumor-specific neoantigens

Calculate Neoantigen Candidates from A Given Sequence for MHC Class2

Description

Calculate Neoantigen Candidates from A Given Sequence for MHC Class2

Usage

MainSeqFragmentClass2(
  input_sequence = NA,
  group_ids = seq(1:length(reference_nm_id)),
  hla_file = "here_is_a_table",
  hla_types = NA,
  file_name_in_hla_table = NA,
  refflat_file = paste(hmdir, "lib/refFlat.txt", sep = "/"),
  refmrna_file = paste(hmdir, "lib/refMrna.fa", sep = "/"),
  hmdir = getwd(),
  job_id = "ID",
  export_dir = paste("result", job_id, "SeqFragment2", sep = "."),
  netMHCIIpan_dir = paste(hmdir, "lib/netMHCIIpan-3.1/netMHCIIpan", sep = "/"),
  peptide_length = c(15),
  reference_nm_id = NA,
  reference_gene_symbol = NA,
  ignore_short = TRUE
)

Arguments

input_sequence	(Required) An input amino acid sequence
group_ids	flag to cluster the same group
hla_file	A tab separated file indicating HLA types. The 1st column is input_file name, and the following columns indicate HLA types. See by data(sample_hla_table_c1); sample_hla_table_c1;
hla_types	Set a list of HLA types
file_name_in_hla_table	If the name (1st column) in HLA table is not the same as input_file, indicate the corresponding name (Default=input_file).
refflat_file	refFlat file to be used in constructing peptide. (Default=paste(hmdir, "lib/refFlat.txt", sep=""). See "https://github.com/hase62/Neoantimon"
refmrna_file	refMrna file to be used in constructing peptide (Default=paste(hmdir, "lib/refMrna.fa", sep=""). See "https://github.com/hase62/Neoantimon"
hmdir	Home directory for the analysis (Default = getwd()).
job_id	Job-Id to be attached in output files (Default = "NO_job_id").
export_dir	The directory will be stored results (Default = "paste("result", file_name_in_hla_table, job_id, sep=".")")
netMHCIIpan_dir	The file directory to netMHCpan (Default="lib/netMHCIIpan-3.2/netMHCIIpan").
peptide_length	Peptide Length to be generated (Default = 8,9,10,11,12,13).
reference_nm_id	Corresponding original sequences that the input sequence is generated. If franctions of peptides generated from the input are included in the indicated protein, such peptides are removed. It can be indicated when gene_symbol is not NA.
reference_gene_symbol	Corresponding original sequences that the input sequence is generated. If franctions of peptides generated from the input are included in the indicated protein, such peptides are removed. It can be indicated when nm_id is not NA.
ignore_short	Ignore to output results of short peptide less than min (peptide_length)

Value

void (Calculated Neoantigen Files will be generated as .tsv files.):

HLA: HLA type used to calculate neoantigen.

Pos: The position of a fraction of peptide used to be evaluated from the full-length peptide.

Gene Gene symbol used to be evaluated in NetMHCpan.

Evaluated_Mutant_Peptide: The mutant peptide to be evaluated.

Evaluated_Mutant_Peptide_Core: The core peptide of the mutant peptide to be evaluated in NetMHCpan.

Mut_EL: EL value for evaluated mutant peptide.

Mut_Rank: Rank value for evaluated mutanat peptide.

Chr: Chromosome Number of the mutation.

NM_ID: NM_ID used to construct peptides from the mutation.

Change: The annotation to be described in .vcf file.

Ref: reference type nucleic acid base.

Alt: alternative type nucleic acid base.

Prob: A probability of reference nucleic acid base described in .vcf file.

Mutation_Prob: A probability of alternative nucleic acid base described in .vcf file.

Exon_Start: The exon start position of the corrsponding NM_ID.

Exon_End: The exon end position of the corrsponding NM_ID.

Mutation_Position: The mutation position of the corrsponding NM_ID.

Total_Depth: The sum depth of the reference and alternative nucleic acid base.

Tumor_Depth: The depth of the alternative nucleic acid base.

Wt_Peptide: The full-length of the wild-type peptide.

Mutant_Peptide: The full-length of the mutant peptide.

Total_RNA: The expression amount of the corresponding RNA.

Tumor_RNA_Ratio: The variant allele frequency of the corresponding RNA.

Tumor_RNA: The modified amount of the corresponding RNA level based on RNA Reads.

Tumor_RNA_based_on_DNA: The modified amount of the corresponding RNA level based on DNA Reads.

MutRatio: The mean value of the cancer cell fraction probability.

MutRatio_Min: The 1% percentile of the cancer cell fraction probability.

MutRatio_Max: The 99% percentile of the cancer cell fraction probability.

P_I: Priority score using the EL. Please use CalculatePriorityScores <- function(result, useRNAvaf = FALSE)

P_R: Priority score using the percentage of rank affinity. Please use CalculatePriorityScores <- function(result, useRNAvaf = FALSE)

P: Priority score implemented in MuPeXI (Bjerregaard et al. 2017). Please use CalculatePriorityScores <- function(result, useRNAvaf = FALSE)

hase62/Neoantimon documentation built on Sept. 21, 2023, 4:23 p.m.