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Example data: Log R ratio from bulk sequencing data

Source: R/data.R
exdata_bulk_lrr.Rd

Data frame containing log R ratio values per genomic segments from bulk sequencing data. Only chromosomes 3, 4 and 8 are present in the exdata example dataset.

Usage

exdata_bulk_lrr

Format

A data frame with the following columns:

CHROM

Chromosome names, e.g. "3", "X".

start

Start position of the segment.

end

End position of the segment.

lrr

Log R ratio of the segment ("cnlr.median" column from facets::fitcncf() $cncf data frame).

Note

Data obtained from whole genome sequencing (WGS) after using facets::fitcncf() from facets "Cellular Fraction and Copy Numbers from Tumor Sequencing" version 0.6.2: $cncf data frame columns chrom, start, end, and cnlr.median.

References

facets package

Shen R, Seshan VE. FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing. Nucleic Acids Res. 2016 Sep 19;44(16):e131. doi: 10.1093/nar/gkw520. PMID: 27270079; PMCID: PMC5027494.