genomeChartSV: genomeChartSV

In Nik-Zainal-Group/signature.tools.lib: signature.tools.lib

genomeChartSV

Description

Plotting of somatic variants using the circlize R package. This plot focuses on structural variants (SVs or rearrangements). Clusters of SVs, if any, are shown on the plot using a different colour for each cluster. If SNVs are available, SNVs within the SV clusters are identified and used to build an SNV mutational catalogue of these localised variants. Moreover, if the bedpe file of the SVs contains data about non-templated insertions and micro-homology deletions at breakpoint junctions then the SV junction catalogue is also built and shown.

Usage

genomeChartSV(
  outfilename,
  SV_bedpe_file = NULL,
  SV_bedpe_table = NULL,
  SNV_vcf_file = NULL,
  SNV_tab_file = NULL,
  SNV_table = NULL,
  PEAK.FACTOR = 10,
  kmin = 10,
  plot_title = NULL,
  genome.v = "hg19"
)

Arguments

outfilename	file where the figure should be plotted. This also determines the file type of the output, use either pdf (recommended) or png
SV_bedpe_file	name of the tab separated bedpe file containing the SVs. The file should contain a rearrangement for each row (two breakpoint positions should be on one row as determined by a pair of mates of paired-end sequencing) and should already be filtered according to the user preference, as all rearrangements in the file will be used and no filter will be applied. The files should contain a header in the first line with the following columns: "chrom1", "start1", "end1", "chrom2", "start2", "end2" and "sample" (sample name). In addition, either two columns indicating the strands of the mates, "strand1" (+ or -) and "strand2" (+ or -), or one column indicating the structural variant class, "svclass": translocation, inversion, deletion, tandem-duplication. The column "svclass" should correspond to (Sanger BRASS convention): inversion (strands +/- or -/+ and mates on the same chromosome), deletion (strands +/+ and mates on the same chromosome), tandem-duplication (strands -/- and mates on the same chromosome), translocation (mates are on different chromosomes). In addition, columns 'non-template' and 'micro-homology' can be specified, including the non-templated insertion or micro-homology deletion sequence, which will be used to build an SV junctions catalogue.
SV_bedpe_table	data frame formatted as in the SV_bedpe_file description
SNV_vcf_file	name of the vcf file containing the SNVs
SNV_tab_file	name of the tab separated file containing the SNVs. Column names should be: chr, position, REF and ALT. If SNV_vcf_file is also specified, these variants will be ignored and the variants in the vcf file will be used instead.
SNV_table	data frame formatted as in the SNV_tab_file description
plot_title	title of the plot. If NULL, then the sample_name will be used as title. Use "", the empty string, to have no title.
genome.v	genome version to use, either hg19 or hg38

Value

all computed results, like catalogues and clustering regions, will be returned

Nik-Zainal-Group/signature.tools.lib documentation built on April 13, 2025, 5:50 p.m.