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

Description Usage Arguments Details Value

Allelic segmentations are estimated for one sample at a time with unfiltered sequencing calls using the package sequenza. This function can handle only a combination of one tumor sample with a matched normal sample.

1	CopySeg_sequenza(x, AD, file.name)

`x`	A `vcfR` object of the sequencing calls. The sample names can be queried from `x`.
`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.

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 segmentations.

Subhayan18/CRUST documentation built on Dec. 18, 2021, 3:03 p.m.