HousekeepersHuman: HousekeepersHuman

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

Functon to retrieve genes of MHCI peptides represented across most tissues/donors/alleles

Usage

HousekeepersHuman(
  df_human,
  NumDonorsperGene = 2,
  NumAllelesperGene = 1,
  topSeq = 100,
  minNumTissues = 14
)

Arguments

df_human	Input data frame usually from GetHumanMHCI data
NumDonorsperGene	Minimum number of donors where a gene was found to be represented by universal (housekeeping) MHCI peptides, Default: 2
NumAllelesperGene	Minimum number of alleles across all donors where a gene was found to be represented by universal (housekeeping) MHCI peptides, Default: 1
topSeq	Selection of the top x peptides measured the most frequently as univeral (housekeeping) from which genes will be determined as universal, Default: 100
minNumTissues	Min number of tissues that must have been sampled for a donor to be considered, Default: 14

Details

The term universal peptide is used synonymously to housekeeping peptide

Value

List containing ggplot2 figures and output data frame

See Also

count ggplot,aes,geom_bar,coord_flip,scale_continuous venn org.Hs.eg.db

Examples

## Not run: 
HousekeepersHuman(df_human)

## End(Not run)

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