MValueTrimmingConfig
- class VmaxBuilder.config.dataclasses.MValueTrimmingConfig(trim_correction_addition: float = 2, trim_percentiles: tuple[float, float] = (2.5, 97.5), trim_threshold: float = 0.585)[source]
Generated: validation needed.
- Description:
Configuration for M_value trimming. To assess trimmability, M_value assumes that
expression data is in linear space (not log transformed), and then checks for each gene across the samples if the high and low percentile values (denoted by the trim_percentiles config) of the gene’s expression differ by more or less than the denoted threshold in log 2 (log2(high/low)). Note that trimmable genes are not automatically trimmed, only marked to be eligible for trimming during IFP allocation.
- Parameters:
trim_correction_addition (float) – Value added to all reactions’ IFP sums during trimming to prevent extremely lowly expressed genes to be denoted as unstable.
trim_percentiles (tuple[float, float]) – Lower and upper percentiles used to determine whether gene is trimmable.
trim_threshold (float) – Threshold used to determine whether gene is trimmable: In particular genes whose upper and lower percentiles after addition of trim_correction_addition are below this threshold will be considered stable enough to be trimmed.
Public Methods
trim_correction_additiontrim_percentilestrim_threshold