GetMouseMHCIdata: GetMouseMHCIdata

In CaronLab/MHCIatlas: Package to reproduce data analysis and further explore the data depicted by Kubiniok et al. 2021 in 'Global Analysis of the Mammalian MHC class I Immunopeptidome at the Organism-Wide Scale'.

Description

Function to retrieve the mouse MHCI tissue draft dataset

Usage

GetMouseMHCIdata(NetMHC_Rank_Threshold = 2, return_all_rawData = FALSE)

Arguments

NetMHC_Rank_Threshold	NetMHCpan4.0 rank threshold value (peptides with binding scores below or equal to this value are selected), Default: 2
return_all_rawData	Logical, TRUE returns the raw dataset while FALSE returns a cleaned up version that is to be used with most functions of the MHCIatlas Rpackage, Default: FALSE

Details

More about the NetMHCpan-4.0 scoring system and MHCI binding prediction can be found here: NetMHCpan-4.0: Improved Peptide–MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data Vanessa Jurtz, Sinu Paul, Massimo Andreatta, Paolo Marcatili, Bjoern Peters and Morten Nielsen The Journal of Immunology (2017) ji1700893; DOI: 10.4049/jimmunol.1700893

Value

Data frame of the human MHCI peptide tissue draft

Examples

## Not run: 
df_mouse<- GetMouseMHCIdata()

## End(Not run)

CaronLab/MHCIatlas documentation built on March 10, 2021, 12:38 a.m.