genic_load: Annotate genic load

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

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)

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