getadjustedsegments: Create a data frame with segment information corresponding to...
In ACE: Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing

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

getadjustedsegments applies model parameters to segment data and returns a data frame with information of the individual segments, scaled according to the model.

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getadjustedsegments(template, QDNAseqobjectsample = FALSE, 
                    cellularity = 1, ploidy = 2, standard, 
                    log = FALSE)

`template`	Object. Either a data frame as created by `objectsampletotemplate`, or a QDNAseq-object
`QDNAseqobjectsample`	Integer. Specifies which sample to analyze from the QDNAseq-object. Required when using a QDNAseq-object as template. Default = FALSE
`cellularity`	Numeric. Used for rescaling bin and segment values. Default = 1
`ploidy`	Integer. Assume the median of segments has this absolute copy number. Default = 2
`standard`	Numeric. Force the given ploidy to represent this raw value. When omitted, the standard will be calculated from the data. When using parameters obtained from `squaremodel`, specify standard = 1
`log`	Logical. When TRUE, log2-values are calculated straigth from raw data, unadjusted! Convenience function to resemble DNAcopy output as used for ABSOLUTE and others. Default = FALSE

The output contains two columns for segment mean. The first is the adjusted segment value, the second (Segment_Mean2) is the mean of the adjusted copy number values. I do not know how the QDNAseq or DNAcopy calculates the segment mean, but there is always a very small difference between the two. The P_log10 is the 10-base log of the two-sided probability that the real segment mean is the integer closest to the segment mean. While this gives an indication of the chance that a segment is subclonal, it should be interpreted with care. Because segments usually comprise many bins, these values can easily be very low. A small bias in the normalization can cause "significant", but not necessarily relevant results.

Returns a data frame with segment information

Jos B. Poell

analyzegenomiclocations, postanalysisloop

## using segmented data from a QDNAseq-object
data("copyNumbersSegmented")
singlemodel(copyNumbersSegmented, QDNAseqobjectsample = 2)
getadjustedsegments(copyNumbersSegmented, QDNAseqobjectsample = 2, 
  cellularity = 0.39)