checknetMHCpan {RHybridFinder}

checknetMHCpan

Description

checknetMHCpan, utilizes the file from the second (PEAKS) run and analyzes the data with netMHCpan in order to provide the peptide binding affinity to different HLA/MHC alleles.

Usage

checknetMHCpan(
  netmhcpan_directory,
  netmhcpan_alleles,
  peptide_rerun,
  HF_step1_output,
  export_files = FALSE,
  export_dir = NULL
)

Arguments

netmhcpan_directory

the directory in which the netMHCpan file is.

netmhcpan_alleles

vector of comma-separated alleles for which these peptides should be analyzed (i.e HLA_alleles_Exp1<- c("HLA-A*02:01", "HLA-A*03:01", "HLA-A24:02"))

peptide_rerun

dataframe containing the results of the second run

HF_step1_output

the HybridFinder output containing the potential splicing categorizations obtained with the HybridFinder function (HybridFinder) based on the matching of fragment pairs of peptides in 1 or 2 proteins. This parameter can be provided either by loading the .csv exported file, or if the results #' object still is in the global environment (i.e results_HF_Exp1), then it can be accessed by simply writing "results_HF_Exp1[[1]]".

export_files

a boolean parameter for exporting the dataframes into files in the next parameter for the output directory, Default: FALSE

export_dir

export_dir the output directory for the results files if export_files=TRUE, Default: NULL

Details

The ability to check the peptide binding affinity to the different MHC/HLA molecules is essential for assessing the antigenicity of all peptides. This function thus uses netMHCpan (Reynisson et al., 2020) for the generation of binding affinty results.

Value

1. netMHCpan results pertaining to the binding affinity of all peptides in the database search results (in long- and wide- format, with data tidying in the wide format in order to compute the amount of HLA molecules to which a peptide is strong/weak/non-binder binder)(dataframe)

2. netMHCpan results pertaining to the binding affinity of the hybrid peptides to the MHC molecules (in long- and wide- format, with data tidying in the wide format in order to compute the amount of HLA molecules to which a peptide is strong/weak/non-binder binder) (dataframe)

3. the database search rerun with the categorizations already determined in step1 (HybridFinder Function)

(datafrane)

Examples

## Not run: 
  results_checknetmhcpan_Exp1<- checknetMHCpan('/usr/local/bin', alleles,
  peptide_rerun, Exp1_HF_results[[1]])
  results_checknetmhcpan_Exp1 <- checknetMHCpan('/usr/local/bin', alleles,
  peptide_rerun, Exp1_HF_results_denovo_w_spliced)

## End(Not run)