QC_output: Example of output generated by clustering of Input_Example

In DeveauP/QuantumClone: Clustering Mutations using High Throughput Sequencing (HTS) Data

Description

Clustering output generated by: QC_output<-One_step_clustering(SNV_list = Input_Example,contamination = c(0,0), nclone_range = 2:5,maxit = 1, save_plot = FALSE,ncores = 1, epsilon = 0.01) On October, 30th 2015

Usage

QC_output

Format

list of lists

EMOutput

Results of Expectation maximization: *fik: probability of a mutation (line) to belong to clone k (column) *weights: proportion of mutations belonging to clone k *centers: cellularity of clone k in sample j *val: value of log-likelihood

filtered.data

input data without mutations removed (missing genotype or genotype not AB if filtered on AB)

cluster

Result of hard clustering: each mutation is attributed to a single clone

DeveauP/QuantumClone documentation built on Oct. 29, 2021, 8:56 a.m.