Get CN Segments. — get_cn_segments • GAMBLR

Retrieve all copy number segments from the GAMBL database that overlap with a single genomic coordinate range.

get_cn_segments(
  region,
  chromosome,
  qstart,
  qend,
  projection = "grch37",
  this_seq_type = "genome",
  with_chr_prefix = FALSE,
  streamlined = FALSE,
  from_flatfile = TRUE
)

Arguments

region: Region formatted like chrX:1234-5678 or X:1234-56789.
chromosome: The chromosome you are restricting to. Required parameter if region is not specified.
qstart: Start coordinate of the range you are restricting to. Required parameter if region is not specified.
qend: End coordinate of the range you are restricting to. Required parameter if region is not specified.
projection: Selected genome projection for returned CN segments. Default is "grch37".
this_seq_type: Seq type for returned CN segments. One of "genome" (default) or "capture".
with_chr_prefix: Boolean parameter for toggling if chr prefixes should be present in the return, default is FALSE.
streamlined: Return a basic rather than full MAF format. Default is FALSE.
from_flatfile: Set to TRUE by default.

Value

A data frame with CN segments for the specified region.

Details

This function returns CN segments for s specified region. There are multiple ways a region can be specified. For example, the user can provide the full region in a "region" format (chr:start-end) to the region parameter. Or, the user can provide chromosome, start and end coordinates individually with chr, start, and end parameters. For more usage examples, refer to the parameter descriptions and examples in the vignettes. Is this function not what you are looking for? Try one of the following, similar, functions; assign_cn_to_ssm, get_cn_states, get_sample_cn_segments

Examples

#Example using chromosome, qstart and qend parameters:
segments_region_grch37 = get_cn_segments(chromosome = "chr8",
                                         qstart = 128723128,
                                         qend = 128774067)
# Example for the capture samples:
capture_segments_region_grch37 = get_cn_segments(
 chromosome = "chr8",
 qstart = 128723128,
 qend = 128774067,
 this_seq_type = "capture"
)

#Example using the regions parameter:
segments_region_hg38 = get_cn_segments(region = "chr8:128,723,128-128,774,067",
                                       projection = "hg38",
                                       with_chr_prefix = TRUE)