CN VAF Plot

Create a genome-wide copy number plot for one sample and (optionally) display mutation VAF.

copy_number_vaf_plot(
  this_sample_id,
  just_segments = FALSE,
  coding_only = FALSE,
  one_chrom,
  genes_to_label,
  this_seq_type = "genome",
  from_flatfile = TRUE,
  use_augmented_maf = TRUE,
  add_chr_prefix = FALSE
)

Arguments

this_sample_id

The sample_id for the sample to plot.

just_segments

Specify whether only the segments will be plotted (instead of mutation VAF). Default is FALSE.

coding_only

Optional. Set to TRUE to restrict to plotting only coding mutations.

one_chrom

Subset plot to one chromosome.

genes_to_label

Optional. Provide a vector of genes to label (if mutated). Can only be used with coding_only (see above).

this_seq_type

Seq type for returned CN segments. One of "genome" (default) or "capture".

from_flatfile

If set to true the function will use flatfiles instead of the database.

use_augmented_maf

Boolean statement if to use augmented maf, default is TRUE.

add_chr_prefix

If TRUE, "chr" prefix will be added to chr column. Default is FALSE.

Value

Nothing

Details

This function takes a sample ID and internally calls assign_cn_to_ssm to get copy number segments for plotting. This plot is visualizing mutation VAFs per default, this can be turned off with setting just_segments to TRUE. This only plots the segments. The user can also restrict the plotted segments to coding regions. To do so, set coding_only= TRUE, and then specify the genes of interest (coding regions) with the genes_to_label (vector of genes).

Examples

#build plot
copy_number_vaf_plot(this_sample_id = "HTMCP-01-06-00422-01A-01D")
#> trying to find output from: battenberg
#> looking for flatfile: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/battenberg_current/99-outputs/seg/genome--projection/HTMCP-01-06-00422-01A-01D--HTMCP-01-06-00422-10A-01D--matched.battenberg.grch37.seg


#coding only
copy_number_vaf_plot(this_sample_id = "HTMCP-01-06-00422-01A-01D",
                     coding_only = TRUE)
#> trying to find output from: battenberg
#> looking for flatfile: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/battenberg_current/99-outputs/seg/genome--projection/HTMCP-01-06-00422-01A-01D--HTMCP-01-06-00422-10A-01D--matched.battenberg.grch37.seg