MainEntireRegionClass1: Calculate A Set All Neoantigen Candidates from A Given Gene...

View source: R/MainEntireRegionClass1.R

MainEntireRegionClass1R Documentation

Calculate A Set All Neoantigen Candidates from A Given Gene Symbol and nm_id for MHC Class1 (Not yet stably available)

Description

Calculate A Set All Neoantigen Candidates from A Given Gene Symbol and nm_id for MHC Class1 (Not yet stably available)

Usage

MainEntireRegionClass1(
  input_nm_id,
  group_ids = seq(1:length(input_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, "EntireRegion1", sep = "."),
  netMHCpan_dir = paste(hmdir, "lib/netMHCpan-4.0/netMHCpan", sep = "/"),
  peptide_length = c(8, 9, 10, 11, 12, 13),
  reading_frame = 1,
  CalculateEL = FALSE,
  ignore_short = TRUE
)

Arguments

input_nm_id

(Required) An input amino acid sequence indicated as NM_ID

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=".")")

netMHCpan_dir

The file directory to netMHCpan (Default="lib/netMHCpan-4.0/netMHCpan").

peptide_length

Peptide Length to be generated (Default = 8,9,10,11,12,13).

reading_frame

The starting frame of the input sequence (Default = 1)

CalculateEL

Whether Calculate EL by NetMHCpan or not.

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.


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