.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
.TH CNVKIT_IMPORT-RNA "1" "July 2023" "cnvkit.py import-rna 0.9.10" "User Commands"
.SH NAME
cnvkit_import-rna \- Convert a cohort of per-gene log2 ratios to CNVkit .cnr format.
.SH DESCRIPTION
usage: cnvkit.py import\-rna [\-h] [\-f NAME] \fB\-g\fR FILE [\-c FILE]
.TP
[\-\-max\-log2 FLOAT] [\-n NORMAL [NORMAL ...]]
[\-d PATH] [\-o FILE] [\-\-no\-gc] [\-\-no\-txlen]
FILES [FILES ...]
.SS "positional arguments:"
.TP
FILES
Tabular files with Ensembl gene ID and number of reads
mapped to each gene, from RSEM or another transcript
quantifier.
.SS "options:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-f\fR NAME, \fB\-\-format\fR NAME
Input format name: 'rsem' for RSEM gene\-level read
counts (*_rsem.genes.results), or 'counts' for generic
2\-column gene IDs and their read counts (e.g. TCGA
level 2 RNA expression).
.TP
\fB\-g\fR FILE, \fB\-\-gene\-resource\fR FILE
Location of gene info table from Ensembl BioMart.
.TP
\fB\-c\fR FILE, \fB\-\-correlations\fR FILE
Correlation of each gene's copy number with
expression. Output of cnv_expression_correlate.py.
.TP
\fB\-\-max\-log2\fR FLOAT
Maximum log2 ratio in output. Observed values above
this limit will be replaced with this value. [Default:
3.0]
.TP
\fB\-n\fR NORMAL [NORMAL ...], \fB\-\-normal\fR NORMAL [NORMAL ...]
Normal samples (same format as `gene_counts`) to be
used as a control to when normalizing and re\-centering
gene read depth ratios. All filenames following this
option will be used.
.TP
\fB\-d\fR PATH, \fB\-\-output\-dir\fR PATH
Directory to write a CNVkit .cnr file for each input
sample. [Default: .]
.TP
\fB\-o\fR FILE, \fB\-\-output\fR FILE
Output file name (summary table).
.SS "To disable specific automatic bias corrections:"
.TP
\fB\-\-no\-gc\fR
Skip GC correction.
.TP
\fB\-\-no\-txlen\fR
Skip transcript length correction.