Export_Summary_IndelSV_perFragments: Export Summary Count from Indel/SV Results

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

Export Summary Count from Indel/SV Results

Description

Export Summary Count from Indel/SV Results

Usage

Export_Summary_IndelSV_perFragments(
  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
)

Arguments

Input	Input file generated from MainSNVClass1,2.
Mut_EL_th	The threshold for mutant peptide to be neoantigen by EL.
Mut_Rank_th	The threshold for mutant peptide to be neoantigen by Rank.
Total_RNA_th	The total RNA expression threshold.
Tumor_RNA_th	The tumor specific RNA expression threshold.
MutRatio_th	The mutation ratio threshold.
Weight	The weight for alterations.
WriteLongIndel	If setting a file name, Write Long Indels of which the p-value is less than 0.05.
IgnoreLongIndel	Ignore Indels of which p-value is less than the indicated value for counting.
DupCount	Count for each different HLA type

Value

Num_Alteration The number of evaluated alterations.

Num_Alteration_Generating_NeoAg The number of evaluated alterations that can generate neoantigen.

Num_Peptide The number of evaluated peptifdes.

Num_Peptide_Generating_NeoAg The number of evaluated peptides that can be neoantigen.

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