export_results: export_HybridFinder_results

In RHybridFinder: Identification of Hybrid Peptides in Immunopeptidomic Analyses

Description

this function allows to export the results list obtained in the HybridFinder() function.

Usage

export_HybridFinder_results(results_list, export_dir)

Arguments

results_list	the results list obtained with the HybridFinder() function.
export_dir	the export directory

Details

In order to be able to have the HybridFinder() results list exported, this function will come in handy. Please note that this function is also part of the HybridFinder() function, therefore if you set export_files=TRUE and you indicate the export directory in export_dir in the HybridFinder() function, you would have the exact same outcome.

Value

exports a folder containing three files

1. the HybridFinder output - the spectra that made it to the end with their respective columns (ALC, m/z, RT, Fraction, Scan) and a categorization column which denotes their potential splice type (-cis, -trans) or whether they are linear (the entire sequence was matched in proteins in the proteome database). Potential cis- & trans-spliced peptide are peptides whose fragments were matched with fragments within one protein, or two proteins, respectively.

2. list of potential hybrid peptides (excluding the linear peptides) (.csv file)

3. the merged proteome consisting of the reference proteome along with the hybrid proteome added at the end of the file with the sequence names following the pattern "sp|denovo_HF_fake_protein" along with a digit at the end (1,2,3,4,4,etc.) (.fasta file)

See Also

write.fasta

Examples

## Not run: 
 export_results(results_HybridFinder_Human_Liver_AUTD17,folder_Human_Liver_AUTD17)

## End(Not run)

RHybridFinder documentation built on Aug. 17, 2021, 5:09 p.m.