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.

   optional arguments:
       -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]