table of contents
| CNVKIT_SEGMETRICS(1) | User Commands | CNVKIT_SEGMETRICS(1) |
NAME¶
cnvkit_segmetrics - Compute segment-level metrics from bin-level log2 ratios.
DESCRIPTION¶
usage: cnvkit segmetrics [-h] -s SEGMENTS [--drop-low-coverage] [-o FILENAME]
- [--mean] [--median] [--mode] [--t-test] [--stdev]
- [--sem] [--mad] [--mse] [--iqr] [--bivar] [--ci] [--pi] [-a ALPHA] [-b BOOTSTRAP] [--smooth-bootstrap] cnarray
positional arguments:¶
- cnarray
- Bin-level copy ratio data file (*.cnn, *.cnr).
optional arguments:¶
- -h, --help
- show this help message and exit
- -s SEGMENTS, --segments SEGMENTS
- Segmentation data file (*.cns, output of the 'segment' command).
- --drop-low-coverage
- Drop very-low-coverage bins before calculations to avoid negative bias in poor-quality tumor samples.
- -o FILENAME, --output FILENAME
- Output table file name.
Statistics available:¶
- --mean
- Mean log2 ratio (unweighted).
- --median
- Median.
- --mode
- Mode (i.e. peak density of bin log2 ratios).
- --t-test
- One-sample t-test of bin log2 ratios versus 0.0.
- --stdev
- Standard deviation.
- --sem
- Standard error of the mean.
- --mad
- Median absolute deviation (standardized).
- --mse
- Mean squared error.
- --iqr
- Inter-quartile range.
- --bivar
- Tukey's biweight midvariance.
- --ci
- Confidence interval (by bootstrap).
- --pi
- Prediction interval.
- -a ALPHA, --alpha ALPHA
- Level to estimate confidence and prediction intervals; use with --ci and --pi. [Default: 0.05]
- -b BOOTSTRAP, --bootstrap BOOTSTRAP
- Number of bootstrap iterations to estimate confidence interval; use with --ci. [Default: 100]
- --smooth-bootstrap
- Apply Gaussian noise to bootstrap samples, a.k.a. smoothed bootstrap, to estimate confidence interval; use with --ci.
| January 2021 | cnvkit segmetrics 0.9.8 |