genomic_locus: Rapid genomic locus annotator for CNV calls

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

Description

genomic_locus add the locus information to a data.table containing CNV calls-like data

Usage

genomic_locus(
  DT_in,
  remote_cytobands = TRUE,
  bands,
  assembly = "hg19",
  keep_str_end = TRUE
)

Arguments

DT_in,	a data.table, usually read_results output.
remote_cytobands,	logical, indicates whether the function should download the CytoBands file or use a local object.
bands,	the local object if remote_cytobands is set to FALSE.
assembly,	character, specify the genomic assembly. Can be either "hg18", "hg19" or "hg38".
keep_str_end,	logical, specify if intermediate columns (locus_start and locus_end) must be kept or discarded.

Details

This function takes a CNVresults object and add a columns containing the genomic locus information. By default the file containing the CytoBands location for the specified assembly are downloaded from UCSC website, but also a local object (as data.table or data.frame) can be used via the argument bands.

Value

a CNVresults, DT_in with the additional column "locus".

Examples

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

## End(Not run)

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