AlleleComp: Copynumber estimation
In Subhayan18/CRUST: Multi-regional clonal deconvolution of tumor sequencing data

Description Usage Arguments Details Value See Also Examples

Allelic segmentations are estimated for one sample at a time with unfiltered sequencing calls.

1	AlleleComp(data, AD, file.name, method, uniform.break)

`data`	A `vcfR` object of the sequencing calls.
`AD`	a `character` deoning ID for depth of the reference allele. This is often separately present in the VCF file. Default is `NULL`.
`file.name`	an optional `character` to define output file name. Default is tumor.sample.
`method`	Algorithm to be used for copy number calculations. options include "apriori" wich uses `CopySeg_sequenza` and "naive" using `CopySeg_falcon`.
`uniform.break`	A numeric value signifying fixed length of the genomic window. Each window is considered as distinct chromosomal segment with edges being the break points for copy number estimation. A good window length is 1Mb (i.e. 1e6)

The function writes a .txt data in working directory with the name defined in file.name used by sequenza. The output file written can be used in conjunction with post variants call sequence file. These can be merged and used for surther analysis with cluster.doc or seqn.scale

A transformed dataframe usable in CloneStrat that represents data on all variants in the .vcf file. It returns summaries on the variants with the collumn CN.profile depicting the estimated allelic compositions.

segment.plot