dynast.estimate
Module Contents
Functions
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Main interface for the estimate command. |
- dynast.estimate.estimate(count_dirs: List[str], out_dir: str, reads: Union[typing_extensions.Literal[complete], List[typing_extensions.Literal[total, transcriptome, spliced, unspliced]]] = 'complete', barcodes: Optional[List[List[str]]] = None, groups: Optional[List[Dict[str, str]]] = None, ignore_groups_for_est: bool = True, genes: Optional[List[str]] = None, downsample: Optional[Union[int, float]] = None, downsample_mode: typing_extensions.Literal[uniform, cell, estimate.group] = 'uniform', cell_threshold: int = 1000, cell_gene_threshold: int = 16, control_p_e: Optional[float] = None, control: bool = False, method: typing_extensions.Literal[pi_g, alpha] = 'alpha', n_threads: int = 8, temp_dir: Optional[str] = None, nasc: bool = False, by_name: bool = False, seed: Optional[int] = None)[source]
Main interface for the estimate command.
- Parameters
- count_dirs
Paths to directories containing count command output
- out_dir
Output directory
- reads
What read group(s) to quantify
- barcodes
Cell barcodes
- groups
Cell groups
- ignore_groups_for_est
Ignore cell groups for final estimation
- genes
Genes to consider
- downsample
Downsample factor (float) or number (int)
- donsample_mode
Downsampling mode
- cell_threshold
Run estimation only for cells with at least this many counts
- cell_gene_threshold
Run estimation for cell-genes with at least this many counts
- control_p_e
Old RNA conversion rate (p_e), estimated from control samples
- control
Whether this is a control sample
- method
Estimation method to use
- n_threads
Number of threads
- temp_dir
Temporary directory
- nasc
Whether to match NASC-seq pipeline behavior
- by_name
Whether to group counts by gene name instead of ID
- seed
Random seed