NAME

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

DESCRIPTION

       usage: cnvkit 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.

   optional arguments:
       -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.