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Example data: Log R ratio from bulk sequencing data

Source: R/data.R
bulk_lrr.Rd

Data frame containing log R ratio values per genomic segments from bulk sequencing data.

Usage

bulk_lrr

Format

A data frame with the following columns:

CHROM

Chromosome in integer format, e.g. 15, 23 (for X chromosome) (character).

start

Start position of the segment (integer).

end

End position of the segment (character).

lrr

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

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.