assembly: Make a 'assembly' object for alternate TxDb, OrgDb,and...

In PhanstielLab/BentoBox: Coordinate-Based Genomic Visualization Package for R

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"
)

PhanstielLab/BentoBox documentation built on June 30, 2024, 12:50 p.m.