orgmsAdd: orgmsAdd Add a new search target in GRange format into...

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

orgmsAdd Add a new search target in GRange format into GRangeList

Description

orgmsAdd Add a new search target in GRange format into GRangeList

Usage

orgmsAdd(orgm, orgTxDB, mycoords.list, orgmsCollection)

Arguments

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
orgTxDB	A data.frame that contains currently TxDB objects, e.g. orgmTxDB.
mycoords.list	A string list with the format of "2:16e7:16.5e7"
orgmsCollection	A GRangesList object that contains a list of search targets in GRange form

Value

orgmsCollection A GRangesList of search targets in GRange form

See Also

Other orgmsCollection: orgmsCollection.init(), orgmsCollectionTestResult

Examples

orgm <- "Hsapiens"
mycoords.list <- "2:15.95e7:16.45e7"
orgm.2 <- "Mmusculus"
mycoords.list.2 <- "2:6.0e7:6.5e7"
orgm.3 <- "Rnorvegicus"
mycoords.list.3 <- "3:4.6e7:5.1e7"

  orgmsList <- orgmsCollection.init (orgmsList)
  orgmsList <- orgmsAdd (orgm, orgmTxDB, mycoords.list, orgmsList)
  orgmsList <- orgmsAdd (orgm.2, orgmTxDB, mycoords.list.2, orgmsList)
  orgmsList <- orgmsAdd (orgm.3, orgmTxDB, mycoords.list.3, orgmsList)
  orgmsList

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