Minimum Error Calibration and Normalization for Copy Number Analysis
A copy number profile usually needs to be calibrated for the position of baseline (normal copy numbers) due to sample impurity and measurement bias. It’s crucial to normalize CN profiles when comparing them in analysis, because usually each profile has a different signal scale.
Mecan4CNA (Minimum Error Calibration and Normalization for Copy Number Analysis) uses an algebraic method to estimate the baseline and the distance between DNA levels (referred to as level distance). It can be used for both single file analysis and multi-file normalization.
- Calibration of a segmentation file, so that the signal of normal is aligned to 2 (0 in log2)
- Estimation of the distance between DNA levels
- Normalizing multiple files to a uniformed signal scale, so that 3 (0.585 in log2) and 1 (-1 in log2) actually correspond to one copy gain and one copy lost
- Needs only a segmentation file (from any platform)
- Detailed results and plots for in-depth analysis
How to install
The easiest way is to install through pip:
pip install mecan4cna mecan4cna --help
How to use
See the manual for details.
mecan4cna -i [SEGMENT_FILE] -o [OUTPUT_PATH]
This will copy 5 example files to the current directory and run with default settings. It invokes the run_mecan_example.sh script, which will also be copied over and can be used as a template for customized analysis.
Usage: mecan4cna [OPTIONS] Options: -i, --input_file FILENAME The input file. -o, --output_path TEXT The path for output files. -n, --normalize Calibrate and normalize the input file. -p, --plot Whether to save the signal histogram. -b, --bins_per_interval INTEGER RANGE The number of bins in each copy number interval. -v, --intervals INTEGER RANGE The number of copy number intervals. --demo Copy example files and run a demo script in the current directory. -pt, --peak_thresh INTEGER RANGE The minimum probes of a peak. -st, --segment_thresh INTEGER RANGE The minimum probes of a segment. --model_steps INTEGER RANGE The incremental step size in modeling. --mpd_coef FLOAT Minimum Peak Distance coefficient in peak detection. --max_level_distance FLOAT The maximum value of level distance. --min_level_distance FLOAT The minimum value of level distance. --min_model_score INTEGER RANGE The minimum value of the model score. --info_lost_ratio_thresh FLOAT The threshold of information lost ratio. --info_lost_range_low FLOAT The low end of information lost range. --info_lost_range_high FLOAT The high end of information lost range. --ld_scaler FLOAT The scaler of level distance in normalization. --help Show this message and exit.
Required options are:
- -i FILENAME
- -o OUTPUTPATH
Input file format
The input should be a segmentation file:
- have at least 5 columns：id, chromosome, start, end, probes and value (in exact order, names do not matter). Any additional columns will be ignored.
- the first line of the file is assumed to be column names, and will be ignored. Do not put empty lines at the beginning of the file.
- be tab separated, without quoted values
id chro start end num_probes seg_mean GSM378022 1 775852 143752373 9992 0.025 GSM378022 1 143782024 214220966 6381 0.1607 GSM378022 2 88585000 144628991 4256 0.0131 GSM378022 2 144635510 146290468 146 0.1432 GSM378022 3 48603 8994748 1469 0.0544
4 files will be created in the output path. If mecan fails to detect anything (not enough aberrant segments or no valid models), only the histogram will be created:
- base_level.txt : contains the estimated baseline and level distance.
- histogram.pdf : a visual illustration of signal distributions.
- models.tsv : a tab separated table that details all information of all models.
- peaks.tsv : a tab separated table shows the determined signal peaks and their relative DNA levels compared to the baseline.
Calibration and normalization
With the -n flag, the input file will be normalized and saved as normalized.tsv.
Import as a python library
import mecan.mecan4cna.algorithms as alg import mecan.mecan4cna.common as comm with open('examples\segment_example_1.tsv', 'r') as fin: segments = comm.file2list(fin) m = alg.mecan() r = m.run(segments)
Error of matplotlib
It seems there is a bug in the latest version (3.0.3) of matplotlib, which may cause problems in OSX. Mecan uses an older verison of matplotlib (2.0.2) to avoid this problem. If you need to use the latest version and run into runtime problems, please check the following links.
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