C++ reference

Breakpoint detection

Find the breakpoints defining copy number regions from a cells by bins matrix.

Parameter name	Description	Default value
d_matrix_file	Path to the counts matrix file, delimiter: ' ', line separator: '\n'	""
n_cells	Number of cells in the input matrix	-
n_bins	Number of bins in the input matrix	-
min_cells	Minimum number of cells to consider for a bin being a breakpoint	4
window_size	Size of the window used in breakpoint detection	10
threshold	Breakpoint calling sensitivity. If -1, stop after computing the LR	3
bp_min	Minimum number of breakpoints	0
bp_limit	Maximum number of breakpoints	300
compute_lr	Boolean indicator of wether the per bin cell-wise breakpoint evidence should be computed	True
lr_file	Path to a matrix containing the evidence for breakpoint at each bin in each cell	""
sp_file	Path to a vector containing the combined evidence for breakpoint at each bin across all cells	""
compute_sp	Boolean indicator of wether the per bin breakpoint evidence should be computed	True
evaluate_peaks	Boolean indicator of wether to evaluate peaks and call breakpoints	True
input_breakpoints_file	Path to file indicating bins which correspond to known breakpoints that must be included. These may be, for example, the chromosome bin coordinates.	""
verbosity	Verbosity of the programme, 0 is non-verbose setting, 1 creates the debug files, 2 writes the logs as well	0
postfix	Postfix to be added to the output files, this is useful when you are running multiple simulations through a workflow management system	""
print_precision	The precision points of the score values to be printed	16

Sample run :

$ ./breakpoint_detection --d_matrix_file ./d_mat.txt --n_bins 1000 --n_cells 400 --window_size 10 --threshold 3.0 --bp_limit 300 --verbosity=1 --evaluate_peaks=True

Inference

Finds the maximum a posteriori tree given a cells by regions matrix.

Parameter name	Description	Default value
region_sizes_file	Path to the file containing the region sizes, each line contains one region size.	""
d_matrix_file	Path to the cells by regions counts matrix file, delimiter: ' ', line separator: '\n'	""
n_iters	Number of iterations	10000
n_cells	Number of cells in the input matrix	-
n_regions	Number of regions in the input matrix	-
ploidy	The ploidy information	2 (diploid, human)
lambda_c	lambda param for the poisson that generates the copy number state of a region	0.2
cluster_sizes_file	Path to the file containing the cluster sizes, where each line contains one cluster size. This only applies if d_matrix_file is a clusters by regions matrix, where each cluster is a summary of its cells' read counts.	""
max_scoring	Whether to use max scoring (true/false).	"true"
seed	Seed	-
postfix	Postfix to be added to the output files, this is useful when you are running multiple simulations through a workflow management system	""
print_precision	The precision points of the score values to be printed	16
----	parameters for the random initialised tree	---
n_nodes	the number of nodes in the random initialised tree	50
lambda_r	lambda param for the poisson that generates the number of regions	0.1
lambda_c	lambda param for the poisson that generates the copy number state of a region	0.2

Sample run :

$ ./inference --n_cells 400 --n_regions 10 --n_iters 100 --n_nodes 10 --ploidy 2 --verbosity 2 --seed 42 --d_matrix_file ./30_d_mat.txt --region_sizes_file ./30_region_sizes.txt

Simulation

Simulates the count matrix. Outputs the count matrix, region sizes, ground truth CNVs and the tree that generated the data.

Parameter name	Description	Default value
n_bins	Number of bins of the input matrix	1000
n_cells	Number of cells	400
n_nodes	Number of nodes of the tree	50
n_regions	Number of regions	50
n_iters	Number of iterations	10000
n_reads	Number of reads per cell	10000
nu	Overdispersion parameter	1
ploidy	The ploidy information	2 (diploid, human)
verbosity	Verbosity of the programme, 0 is non-verbose setting, 1 creates the debug files, 2 writes the inference logs as well, 3 writes the tree logs on top	0
seed	Seed	-
postfix	Postfix to be added to the output files, this is useful when you are running multiple simulations through a work flow management system	""
print_precision	The precision points of the score values to be printed	16

Sample run :

$ ./simulation --n_cells 400 --n_bins 1000 --n_regions 10 --n_nodes 10 --n_reads 100000 --ploidy 2 --verbosity 2  --seed 42 --print_precision 32

Test

Runs the validation tests and writes the results to the standard output and error streams.

Sample run :

$ ./tests