immuno_regions {CNVgears} | R Documentation

## Retrieve genomic regions of consecutive immunoglobulin genes

### Description

Retrieve genomic regions of consecutive immunoglobulin genes

### Usage

    immuno_regions(biotype = NULL, n_genes = 5, mart = NULL)

### Arguments

`biotype,` | vector of character, is used to filter the genes based on `gene_biotype` from to `biomaRt::getBM`. By default all the immunoglobulin biotypes al listed in Genecode <https://www.gencodegenes.org/pages/biotypes.html>. If the user specify one or more values only those are used.
`n_genes,` | integer, number of minimum consecutive genes required to construct an "immunoglobulin region", default is 5.
`mart,` | user provided mart (from `biomaRt::useMart` function). For older assemblies the user must manually retrieve the correct mart via `biomaRt`. `immuno_regions` is used to construct a `data.table` of genomic regions where all the consecutive gene have an immunoglobulin (or user specified). The output can be used as a blacklist in `cleaning_filter`.

### Value

a list with two element, the first is a `data.table` containing the actual regions (to be passed to `cleaning_filter` for example), the second is the full genes list (for the required biotypes), again as `data.table`.

### Examples

    ## Not run:
    DT <- immuno_regions(biotype = c("IG_C_gene", "IG_D_gene"))

    ## End(Not run)

[Package CNVgears version 1.0.0 Index]