GetHumanMHCIdata: GetHumanMHCIdata

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 human MHCI tissue draft dataset

Usage

GetHumanMHCIdata(
  NetMHC_Rank_Threshold = 2,
  return_all_rawData = FALSE,
  omitThymus = TRUE
)

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
omitThymus	TRUE removes Thymus tissue from data, default is TRUE

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_human<- GetHumanMHCIdata()

## End(Not run)

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