cnvkit_genemetrics - Identify targeted genes with copy number gain
or loss.
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] [--stdev] [--sem] [--mad] [--mse] [--iqr] [--bivar] [--ci] [--pi]
[-a ALPHA] [-b BOOTSTRAP] filename
- filename
- Processed sample coverage data file (*.cnr), the output of the 'fix'
sub-command.
- -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.
- --mean
- Mean log2 value (unweighted).
- --median
- Median.
- --mode
- Mode (i.e. peak density of log2 values).
- --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]