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

Description Usage Arguments Details Value Note Author(s) See Also Examples

View source: R/ACE.R

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

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analyzegenomiclocations(segmentdf, Chromosome, Position, 
                        Frequency, cellularity)

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

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.

Author(s)

Jos B. Poell

See Also

getadjustedsegments, linkvariants

Examples

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## 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)

ACE documentation built on Nov. 8, 2020, 5:30 p.m.