ConservationMouse: ConservationMouse

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) MHCI peptides

Usage

ConservationMouse(
  df_mouse,
  pathBW_mouse = "~/Downloads/mm10.60way.phastCons.bw",
  samplesize = 2000,
  returnplots = TRUE
)

Arguments

df_mouse	Mouse MHCI dataset, usually output from the function 'GetMouseMHCIdata'
pathBW_mouse	path to the BigWig file mm10.60way.phastCons.bw downloadable from https://genome.ucsc.edu/, Default: '~/Downloads/mm10.60way.phastCons.bw'
samplesize	Number of tissue specific genes that will be randomly selected to compute conservation, Default: 2000
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.Mmusculus.UCSC.mm10.knownGene org.Mm.eg.db transcripts,transcriptsBy ggplot,aes,scale_colour_brewer,geom_path,facet_grid,theme,margin,labs ggdraw as.ggplot

Examples

## Not run: 
cons_m<-ConservationMouse(df_mouse,samplesize = 200)

## End(Not run)

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