step2_wo_netMHCpan: step2_wo_netMHCpan
In RHybridFinder: Identification of Hybrid Peptides in Immunopeptidomic Analyses

Description Usage Arguments Details Value Examples

View source: R/step2_wo_netMHCpan.R

This function helps retrieve the categorizations for the peptides from step 1 and apply them to those that are matched in the second database search.

step2_wo_netMHCpan(
  peptide_rerun,
  HF_step1_output,
  export_files = FALSE,
  export_dir = NULL
)

`peptide_rerun`	dataframe containing the results of the second database PEAKS search.
`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

In special cases where the PC runs on windows OS, since it would only be possible to use the web version of netMHCpan, this function returns the peptide input file for the webversion of netMHCpan. Also, this function outputs the database search rerun results with their categorizations (into potentially cis and potentially trans) obtained from the first step (HybridFinder).

the input file for the web version of netMHCpan (dataframe)
the database search rerun with the categorizations already determined in the previous step. (character vector)

if (interactive()) {
data(package="RHybridFinder", "db_rerun_Human_Liver_AUTD17")
results_checknetmhcpan_Human_Liver_AUTD17<- step2_wo_netMHCpan(db_rerun_Human_Liver_AUTD17,
    results_HybridFinder_Human_Liver_AUTD17[[1]])
}