.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.10.
.TH CNVKIT_GENEMETRICS "1" "March 2019" "cnvkit_genemetrics 0.9.5" "User Commands"
.SH NAME
cnvkit_genemetrics \- Identify targeted genes with copy number gain or loss.
.SH DESCRIPTION
usage: cnvkit genemetrics [\-h] [\-s SEGMENT] [\-t THRESHOLD] [\-m MIN_PROBES]
.TP
[\-\-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
.SS "positional arguments:"
.TP
filename
Processed sample coverage data file (*.cnr), the
output of the 'fix' sub\-command.
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-s\fR SEGMENT, \fB\-\-segment\fR SEGMENT
Segmentation calls (.cns), the output of the 'segment'
command).
.TP
\fB\-t\fR THRESHOLD, \fB\-\-threshold\fR THRESHOLD
Copy number change threshold to report a gene
gain/loss. [Default: 0.2]
.TP
\fB\-m\fR MIN_PROBES, \fB\-\-min\-probes\fR MIN_PROBES
Minimum number of covered probes to report a
gain/loss. [Default: 3]
.TP
\fB\-\-drop\-low\-coverage\fR
Drop very\-low\-coverage bins before segmentation to
avoid false\-positive deletions in poor\-quality tumor
samples.
.TP
\fB\-y\fR, \fB\-\-male\-reference\fR, \fB\-\-haploid\-x\-reference\fR
Assume inputs were normalized to a male reference
(i.e. female samples will have +1 log\-coverage of
chrX; otherwise male samples would have \fB\-1\fR chrX).
.TP
\fB\-x\fR {m,y,male,Male,f,x,female,Female}, \fB\-\-sample\-sex\fR {m,y,male,Male,f,x,female,Female}, \fB\-g\fR {m,y,male,Male,f,x,female,Female}, \fB\-\-gender\fR {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).
.TP
\fB\-o\fR FILENAME, \fB\-\-output\fR FILENAME
Output table file name.
.SS "Statistics available:"
.TP
\fB\-\-mean\fR
Mean log2 value (unweighted).
.TP
\fB\-\-median\fR
Median.
.TP
\fB\-\-mode\fR
Mode (i.e. peak density of log2 values).
.TP
\fB\-\-stdev\fR
Standard deviation.
.TP
\fB\-\-sem\fR
Standard error of the mean.
.TP
\fB\-\-mad\fR
Median absolute deviation (standardized).
.TP
\fB\-\-mse\fR
Mean squared error.
.TP
\fB\-\-iqr\fR
Inter\-quartile range.
.TP
\fB\-\-bivar\fR
Tukey's biweight midvariance.
.TP
\fB\-\-ci\fR
Confidence interval (by bootstrap).
.TP
\fB\-\-pi\fR
Prediction interval.
.TP
\fB\-a\fR ALPHA, \fB\-\-alpha\fR ALPHA
Level to estimate confidence and prediction intervals;
use with \fB\-\-ci\fR and \fB\-\-pi\fR. [Default: 0.05]
.TP
\fB\-b\fR BOOTSTRAP, \fB\-\-bootstrap\fR BOOTSTRAP
Number of bootstrap iterations to estimate confidence
interval; use with \fB\-\-ci\fR. [Default: 100]