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

Description Usage Arguments Details Value See Also

NGS probes are extracted rom a vcfR object, scaled and bias corrected to optimize estimatio of allelelic composition. This function can handle only a combination of one tumor sample with a matched normal sample. Analysis is performed using the package falcon

1	CopySeg_falcon(data, AD, file.name, uniform.break)

`data`	A `vcfR` object with one normal and one tumor sample. The AD element of the FORMAT field is a manadatory input
`AD`	a `character` denoting ID for depth of the reference allele.
`file.name`	A `character` string. this name will be used to save the scaled and unscaled relative coverage plot along with the final copy number estimate plot in the working directory
`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.

This function uses falcon to estimate allele specific copy number of all sequeneced probes. Subsequently sliding window algorithm is used to generate chromosomal segments with precicted distinct copynumbers. The relative coverages are sclaed with GC content of the binned windows

A list of two data frames that is further used to obtain the allelic segmentation plot

Benjamini et al., 2012 with a loess regression loess.

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