assembly {plotgardener} | R Documentation

## Make a `assembly` object for alternate TxDb, OrgDb,and BSgenome genomic annotation packages

### Description

Make a `assembly` object for alternate TxDb, OrgDb,and BSgenome genomic annotation packages

### Usage

    assembly(
        Genome,
        TxDb,
        OrgDb,
        gene.id.column = "ENTREZID",
        display.column = "SYMBOL",
        BSgenome = NULL
    )

### Arguments

`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 `gene.id.column = "ENTREZID"`.
`display.column` | String of the OrgDb column name that refers to the type of gene symbol to be displayed in plots. Default value is `display.column = "SYMBOL"`.
`BSgenome` | String of the desired BSgenome package name.

### Value

Returns a `assembly` object containing all input parameters.

### See Also

TxDb, OrgDb-class, BSgenome

### Examples

    ## 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"
    )

[Package plotgardener version 1.0.17 Index]