View source: R/MainEntireRegionClass2.R
MainEntireRegionClass2 | R Documentation |
Calculate A Set All Neoantigen Candidates from A Given Gene Symbol and nm_id for MHC Class2 (Not yet stably available)
MainEntireRegionClass2(
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, "EntireRegion2", sep = "."),
netMHCIIpan_dir = paste(hmdir, "lib/netMHCIIpan-3.1/netMHCIIpan", sep = "/"),
peptide_length = c(15),
reading_frame = 1,
CalculateEL = FALSE,
ignore_short = TRUE
)
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=".")") |
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). |
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) |
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.
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