analyzegenomiclocations: Retrieve adjusted copy number information for specific...

In tgac-vumc/ACE: Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing

Retrieve adjusted copy number information for specific genomic locations

Description

analyzegenomiclocations searches an adjusted segment data frame for the specified genomic locations and reports the associated segment mean as "Copynumbers". If frequency of a variant is given (in percentage), mutant copies are also calculated. Make sure the specified cellularity is the same number as was used to create the adjusted segment data frame.

Usage

analyzegenomiclocations(segmentdf, Chromosome, Position, 
                        Frequency, cellularity, sgc = c())

Arguments

segmentdf	Data frame. Output of getadjustedsegments
Chromosome	Vector. Specifies the chromosome(s)
Position	Numeric vector. Specifies the base position(s) of interest
Frequency	Numeric vector. Optional. Used (in conjuction with cellularity) to calculate mutant copies. Enter a percentage.
cellularity	Numeric. Only required when calculating mutant copies. Use same number as used with getadjustedsegments
sgc	Integer or character vector. Specify which chromosomes occur with only a single copy in the germline

Details

The formula that calculates mutant copies only works if the variant is not present in normal tissue. In other words, make sure variants are not of germline origin. If you are interested in a heterozygous germline variant, you can calculate the "mutant copies" by subtracting (1/cellularity - 1).

Value

Returns a data frame with Chromosome, Position, Copynumbers. When Frequency is given as an argument, also returns Mutant_copies.

Note

Chromosome, Position, and Frequency can be single values or vectors. In the latter case, they need to be of equal length. Make sure the position you enter matches with the genome build used for alignment / binning of sequence reads.

When analyzing genomic locations on sex chromosomes of a male individual, make sure to specify sgc = c("X","Y")

Author(s)

Jos B. Poell

See Also

getadjustedsegments, linkvariants

Examples

## using segmented data from a QDNAseq-object
data("copyNumbersSegmented")
segmentdf <- getadjustedsegments(copyNumbersSegmented, 
  QDNAseqobjectsample = 2, cellularity = 0.39)
analyzegenomiclocations(segmentdf, Chromosome = 5, Position = 26365569)
analyzegenomiclocations(segmentdf, Chromosome = 5, Position = 26365569, 
  Frequency = 25, cellularity = 0.39)

tgac-vumc/ACE documentation built on Nov. 29, 2022, 12:15 a.m.