segments

Copy number segmentation matrix obtained as average among G0G1 cells.

datasets

Given an RNA-seq derived cell-by-gene matrix and an DNA-seq derived copy number segmentation, LIAYSON predicts the number of clones present in a tumor, their size, the copy number profile of each clone and the clone membership of each single cell (Andor, N. & Lau, B., et al. (2018) <doi:10.1101/445932>).

Noemi Andor

liayson

Linking Singe-Cell Transcriptomes Atween Contemporary
Subpopulation Genomes

segments function

Matrix in which each row corresponds to a copy number segment as calculated by a circular binary segmentation algorithm. Has to contain at least the following column names: 
 chr - chromosome; 
 startpos - the first genomic position of a copy number segment; 
 endpos - the last genomic position of a copy number segment; 
 CN_Estimate - the copy number estimated for each segment.

Format

Bulk copy number profile of NCI-N87 cell line. — segments

Matrix in which each row corresponds to a copy number segment as calculated by a circular binary segmentation algorithm. Has to contain at least the following column names: 
 chr - chromosome; 
 startpos - the first genomic position of a copy number segment; 
 endpos - the last genomic position of a copy number segment; 
 CN_Estimate - the copy number estimated for each segment.

segments: Bulk copy number profile of NCI-N87 cell line.

Description

Usage

Arguments

Format