CNVKIT_GENEMETRICS

NAME

cnvkit_genemetrics - Identify targeted genes with copy number gain or loss.

DESCRIPTION

usage: cnvkit genemetrics [-h] [-s SEGMENT] [-t THRESHOLD] [-m MIN_PROBES]
[--drop-low-coverage] [-y]

[-x {m,y,male,Male,f,x,female,Female}] [-o FILENAME] [--mean] [--median] [--mode] [--ttest] [--stdev] [--sem] [--mad] [--mse] [--iqr] [--bivar] [--ci] [--pi] [-a ALPHA] [-b BOOTSTRAP] filename

positional arguments:

filename

Processed sample coverage data file (*.cnr), the output of the ’fix’ sub-command.

options:

-h, --help

show this help message and exit

-s SEGMENT, --segment SEGMENT

Segmentation calls (.cns), the output of the ’segment’ command).

-t THRESHOLD, --threshold THRESHOLD

Copy number change threshold to report a gene gain/loss. [Default: 0.2]

-m MIN_PROBES, --min-probes MIN_PROBES

Minimum number of covered probes to report a gain/loss. [Default: 3]

--drop-low-coverage

Drop very-low-coverage bins before segmentation to avoid false-positive deletions in poor-quality tumor samples.

-y, --male-reference, --haploid-x-reference

Assume inputs were normalized to a male reference (i.e. female samples will have +1 log-coverage of chrX; otherwise male samples would have -1 chrX).

-x {m,y,male,Male,f,x,female,Female}, --sample-sex
{m,y,male,Male,f,x,female,Female}, -g {m,y,male,Male,f,x,female,Female},
--gender {m,y,male,Male,f,x,female,Female}

Specify the sample’s chromosomal sex as male or female. (Otherwise guessed from X and Y coverage).

-o FILENAME, --output FILENAME

Output table file name.

Statistics available:

--mean

Mean log2-ratio (unweighted).

--median

Median.

--mode

Mode (i.e. peak density of log2 ratios).

--ttest

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]