table of contents
| CNVKIT_GENEMETRICS(1) | User Commands | CNVKIT_GENEMETRICS(1) |
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]
| January 2021 | cnvkit genemetrics 0.9.8 |