This R package contains mini datasets for running tests and examples in the rock R package.
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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:
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HCC2218 BAF values from AMBER.
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HCC2218 CNVkit cnr file (first 1,000 values from chr22)
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AZ300 cancer gene panel.
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The above datasets can be accesed with
system.file("extdata", <file-name>, package = "pebbles")
.
?pebbles::chr_info
?pebbles::circos_data
e.g. system.file("templates", "circos", "circos_sv.conf")