NAME

       cnvkit_import-rna - Convert a cohort of per-gene log2 ratios to CNVkit .cnr format.

DESCRIPTION

       usage: cnvkit.py import-rna [-h] [-f NAME] -g FILE [-c FILE]

       [--max-log2 FLOAT] [-n NORMAL [NORMAL ...]]
              [-d PATH] [-o FILE] [--no-gc] [--no-txlen] FILES [FILES ...]

   positional arguments:
       FILES  Tabular  files  with Ensembl gene ID and number of reads mapped to each gene, from RSEM or another
              transcript quantifier.

   options:
       -h, --help
              show this help message and exit

       -f NAME, --format 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).

       -g FILE, --gene-resource FILE
              Location of gene info table from Ensembl BioMart.

       -c FILE, --correlations FILE
              Correlation of each gene's copy number with expression. Output of cnv_expression_correlate.py.

       --max-log2 FLOAT
              Maximum  log2  ratio in output. Observed values above this limit will be replaced with this value.
              [Default: 3.0]

       -n NORMAL [NORMAL ...], --normal 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.

       -d PATH, --output-dir PATH
              Directory to write a CNVkit .cnr file for each input sample. [Default: .]

       -o FILE, --output FILE
              Output file name (summary table).

   To disable specific automatic bias corrections:
       --no-gc
              Skip GC correction.

       --no-txlen
              Skip transcript length correction.

cnvkit.py import-rna 0.9.10                         July 2023                               CNVKIT_IMPORT-RNA(1)