tnbc.xenograft.SA494.T: Tripple Negative breast cancer Xenograft, sample SA494,...

In sohrabsa/ddclone: Joint statistical inference of clonal populations from single cell and bulk tumour sequencing data

Description

A dataset containing the allele counts and genotypes from a Tripple negative breast cancer study (see Eirew P, Steif A, Khattra J, Ha G, Yap D, Farahani H, et al. Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution. Nature. 2014;.)

Usage

tnbc.xenograft.SA494.T

Format

A list of 5 variables:

• mutCounts: An integer matrix, with columns corresponding to the genomic loci. First and second rows contain the reference and variant alelle counts respectively.

• psi: The copy number at this genomic locus, encoded as a list, each element of which is a list of 3, gV, gN, and gR, corresponding to variant Copy Number (CN), reference genotype CN, and normal CN. gV is a string in an alphabet of A,B, where the number of A-s denotes the major and the number of B-s denotes the minor CN respectively.

• filteredMutMatrix: A binary genotype-locus matrix, with element [i,j] is one if genotype i is mutated at locus j and is zero otherwise.

• mutPrevalence: For internal use of the package.

• missingIndx: For internal use of the package.

sohrabsa/ddclone documentation built on May 30, 2019, 6:08 a.m.