cnvkit_import-rna

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 ...]

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

-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).