ConservationHuman: ConservationHuman

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 calculate conservation rates of genes representing tissue specific MHCI peptides versus genes representing universal (found across all or most tissues/donors) MHCI peptides

Usage

ConservationHuman(
  df_human,
  HumanHousekeepers,
  pathBW_human = "~/Downloads/hg38.phastCons100way.bw",
  samplesize = 2000,
  quantile = 4,
  ts_DonorSpecific = FALSE,
  MinTissuesPerDonor = 15,
  returnplots = TRUE
)

Arguments

df_human	Human MHCI dataset, usually output from the function GetHumanMHCIdata
HumanHousekeepers	List object from the function HousekeepersHuman
pathBW_human	Path to bigwig file containing human PhastCons conservation scores, Default: '~/Downloads/hg38.phastCons100way.bw'
samplesize	Number of tissue specific genes that will be randomly selected to compute conservation, Default: 2000
quantile	Intensity quantile above which tissue specific peptides will be chosen (4 means that only the 25 percent most intense peptides are considered, 1 means that all peptides are considered), Default: 4
ts_DonorSpecific	Logical value to set if tissue specific (ts) peptides are filtered donor by donor (TRUE) or across all donors (FALSE), Default: FALSE
MinTissuesPerDonor	Peptide must be present in samples from a donor for which the specified minimum number of tissues was measured, Default: 15
returnplots	Logical value to return or not return visualization object in output list, Default: TRUE

Details

Output data using the default values are provided with the package and can be accessed throug running the function 'mkFigure5'

Value

List containing ggplot2 objects (plots) and output data to create plots

See Also

TxDb.Hsapiens.UCSC.hg38.knownGene count org.Hs.eg.db transcripts,transcriptsBy ggplot,aes,scale_colour_brewer,geom_path,facet_grid,theme,margin,labs ggdraw,draw_plot,draw_plot_label as.ggplot

Examples

## Not run: 
cons_h<-ConservationHuman(df_human,HousekeepersHuman(df_human),samplesize=200)

## End(Not run)

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