DOKK / manpages / debian 10 / cnvkit / cnvkit-segmetrics.1.en

cnvkit_segmetrics - Compute segment-level metrics from bin-level log2 ratios.

usage: cnvkit segmetrics [-h] -s SEGMENTS [--drop-low-coverage] [-o FILENAME]

[--mean] [--median] [--mode] [--stdev] [--sem]
[--mad] [--mse] [--iqr] [--bivar] [--ci] [--pi] [-a ALPHA] [-b BOOTSTRAP] cnarray

Bin-level copy ratio data file (*.cnn, *.cnr).

show this help message and exit
Segmentation data file (*.cns, output of the 'segment' command).
Drop very-low-coverage bins before calculations to avoid negative bias in poor-quality tumor samples.
Output table file name.

Mean log2 value (unweighted).
Mode (i.e. peak density of log2 values).
Standard deviation.
Standard error of the mean.
Median absolute deviation (standardized).
Mean squared error.
Inter-quartile range.
Tukey's biweight midvariance.
Confidence interval (by bootstrap).
Prediction interval.
Level to estimate confidence and prediction intervals; use with --ci and --pi. [Default: 0.05]
Number of bootstrap iterations to estimate confidence interval; use with --ci. [Default: 100]
March 2019 cnvkit_segmetrics 0.9.5