cnvkit-segmetrics1

positional arguments:

cnarray

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

options:

-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.