synvizPlotData: synvizPlotData A data retrive function to prepare the data...

In DPP4ResearchGroup/SyntenyViz: Visualize the synteny of a gene structure across species

synvizPlotData A data retrive function to prepare the data for synvizPlot.

Description

synvizPlotData A data retrive function to prepare the data for synvizPlot.

Usage

synvizPlotData(mycoords.gr, orgm)

Arguments

mycoords.gr

A target search range in form of a GRanges object

orgm

An organism that of interest. Options include: Btaurus(Bt) - Bos taurus - Cow Celegans(Ce) - Caenorhabditis elegans - Roundworm Cfamiliaris(Cf) - Canis familiaris - Dog Dmelanogaster(Dm) - Drosophila melanogaster - Fruitfly Drerio(Dr) - Danio rerio - Zebrafish Ggallus(Gg) - Gallus gallus - Chicken Hsapiens(Hs) - Homo Sapiens - Human Mmulatta(Mmu) - Macaca mulatta - Rhesus macaque Mmusculus(Mm) - Mus musculus - House mouse Ptroglodytes(Pt) - Pan troglodytes - Chimpanzee Rnorvegicus(Rn) - Rattus norvegicus - Brown rat Scerevisiae(Sc) - Saccharomyces cerevisiae - Brewer's yeast Sscrofa(Ss) - Sus scrofa - Wild swine

Value

A list that consists of AnnotationTrack, GenomeAxisTrack and IdeogramTrack to feed into the function synvizPlot

See Also

Other SynvizPlot: multisynvizPlots(), synvizDataTest, synvizPlot()

Examples

  orgm <- "Hsapiens"
  mycoords.list <- "2:16e7:16.5e7"
  mycoords.gr <- coordFormat (mycoords.list)
  synvizPlotData (mycoords.gr, orgm)

DPP4ResearchGroup/SyntenyViz documentation built on Nov. 19, 2023, 1:16 a.m.