genomic_locus {CNVgears} | R Documentation |
genomic_locus
add the locus information to a data.table
containing CNV calls-like data
genomic_locus( DT_in, remote_cytobands = TRUE, bands, assembly = "hg19", keep_str_end = TRUE )
DT_in, |
a |
remote_cytobands, |
logical, indicates whether the function should download the CytoBands file or use a local object. |
bands, |
the local object if |
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. |
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
.
a CNVresults
, DT_in
with the additional column "locus".
## Not run: DT <- genomic_locus(penn_22) ## End(Not run)