genomic_locus {CNVgears} | R Documentation

## Rapid genomic locus annotator for CNV calls

### 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)

[Package CNVgears version 1.0.0 Index]