assembly {plotgardener} | R Documentation |
assembly
object for alternate TxDb, OrgDb,and BSgenome
genomic annotation packagesMake a assembly
object for alternate TxDb, OrgDb,and BSgenome
genomic annotation packages
assembly( Genome, TxDb, OrgDb, gene.id.column = "ENTREZID", display.column = "SYMBOL", BSgenome = NULL )
Genome |
String indicating the name of the genome assembly. |
TxDb |
String of existing TxDb package name or a TxDb object. |
OrgDb |
String of the desired OrgDb package name. |
gene.id.column |
String of the TxDb column name that refers to
the given TxDb gene IDs.
Default value is |
display.column |
String of the OrgDb column name that refers to
the type of gene symbol to be displayed in plots.
Default value is |
BSgenome |
String of the desired BSgenome package name. |
Returns a assembly
object containing all input parameters.
## Create a custom `assembly` object for hg38/GRCh38 packages newAssembly <- assembly( Genome = "hg38_GRCh38", TxDb = "TxDb.Hsapiens.UCSC.hg38.knownGene", OrgDb = "org.Hs.eg.db", BSgenome = "BSgenome.Hsapiens.NCBI.GRCh38" )