immuno_regions: Retrieve genomic regions of consecutive immunoglobulin genes

In SinomeM/CNVgears: A Framework to Combine, Analize and Interpret CNVs Calling Results

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)

SinomeM/CNVgears documentation built on Nov. 21, 2021, 5:34 a.m.