genic_load {CNVgears} | R Documentation

## Annotate genic load

### Description

Annotate genic load

### Usage

    genic_load(DT_in, biotypes = "protein_coding", mart = NULL)

### Arguments

`DT_in,` | a `data.table` consisting of CNVs calling results.
`biotypes,` | character vector of Genecode biotypes, default value is "protein_coding".
`mart,` | user specified `biomaRt::useMart()` object. Used if DT_in is assembly (e.g. hg19) require older Ensembl releases. If NA the latest release available by `biomaRt::useMart()` is used. This function takes a `CNVresults` object as input and add two additional columns representing the genic content of each call, i.e. "genes" and "n_genes". The genes considered can be changed using the `biotypes` parameter depending on which types of genes is the user interested in. At the moment, genes a stored as a "-" separated list of Ensembl IDs.

### Value

the `CNVresults` object `DT_in` with additional columns: genes and n_genes.

### Examples

    ## Not run:
    DT <- genic_load(penn_22)

    ## End(Not run)

[Package CNVgears version 1.0.0 Index]