From_freq_to_cell: Wrap-up function

Description

Function that computes the most likely position for each mutation based on the genotype

Usage

From_freq_to_cell(SNV_list, FREEC_list = NULL, Sample_names,
  Genotype_provided = FALSE, save_plot = TRUE, contamination, ncores = 4,
  restrict.to.AB = FALSE, output_directory = NULL,
  force.single.copy = FALSE)

Arguments

SNV_list

A list of dataframes (one for each sample), with as columns : (for the first column of the first sample the name of the sample), the chromosome "Chr",the position of the mutation "Start", the number of reads supporting the mutation "Alt", the depth of coverage at this locus "Depth", and if the output from FREEC for the samples are not associated, the genotype "Genotype".

FREEC_list

list of dataframes from FREEC for each samples (usually named Sample_ratio.txt), in the same order as SNV_list

Sample_names

Name of the samples

Genotype_provided

If the FREEC_list is provided, then should be FALSE (default), otherwise TRUE

save_plot

Should the plots be saved? Default is TRUE

contamination

Numeric vector describind the contamination in all samples (ranging from 0 to 1). Default is 0. No longer used for clustering.

ncores

Number of cores to be used during EM algorithm

restrict.to.AB

Should the analysis keep only sites located in A and AB sites in all samples?

output_directory

Directory in which to save results

force.single.copy

Should all mutations in overdiploid regions set to single copy? Default is FALSE