README.md

In pdiakumis/umccr.facets.gc: Datasets for running tests and examples in the rock R package

pebbles

This R package contains mini datasets for running tests and examples in the rock R package.

Raw Data

• Whole exome sequencing data from the HCC2218 breast carcinoma cell line (available via https://github.com/Illumina/canvas#demo-tumor-normal-enrichment-workflow) were analysed using the bcbio toolkit and/or individual tools. Processed output from the following files is available:

  • CNVkit CNV calls: "HCC2218_cnvkit-call.cns"
  • FACETS CNV calls: "HCC2218_facets_cncf.tsv"
  • Manta SV calls: "HCC2218_manta.vcf"
  • PURPLE CNV calls: "HCC2218_purple.cnv.tsv"
  • TitanCNA CNV calls: "HCC2218_titan.segs.tsv"

• HCC2218 BAF values from AMBER.

• HCC2218 CNVkit cnr file (first 1,000 values from chr22)

• AZ300 cancer gene panel.

• The above datasets can be accesed with system.file("extdata", <file-name>, package = "pebbles").

Exported Data

• ?pebbles::chr_info
• ?pebbles::circos_data

Circos Templates

• Templates for circos - also see rock for use cases.

e.g. system.file("templates", "circos", "circos_sv.conf")

pdiakumis/umccr.facets.gc documentation built on Oct. 18, 2020, 7:37 a.m.