geopagg 0.3.1

An implementation of the geopagg algorithm for p-value aggregation of sgRNAs across gene groupings
Documentation 
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use derive_new::new;
use log::error;

use crate::{
    config::WeightConfig,
    math::{aggregate_pvalues, arithmetic_mean},
    results::GeneResult,
};

/// Represents an amalgam group in the GeoPAGG algorithm
///
/// An amalgam group is a collection of randomly selected sgRNAs used for
/// comparison with actual gene groups to calculate empirical FDR.
#[derive(new, Debug)]
pub struct Amalgam {
    /// Number of sgRNAs in this amalgam group
    membership_size: usize,
    /// Index of this amalgam within its size group
    draw_index: usize,
    /// P-values of the sgRNAs in this amalgam
    pvalues: Vec<f64>,
    /// Log fold changes of the sgRNAs in this amalgam
    logfc: Vec<f64>,
    /// Configuration for p-value weighting
    weight_config: WeightConfig,
}

impl TryFrom<Amalgam> for GeneResult {
    type Error = crate::Error;

    /// Converts an Amalgam into a GeneResult
    ///
    /// This conversion aggregates the p-values and log fold changes of the amalgam
    /// and creates a unique identifier for the amalgam.
    fn try_from(amalgam: Amalgam) -> Result<Self, Self::Error> {
        if amalgam.membership_size == 0 {
            error!("Found a membership size of zero for amalgam: {:?}", amalgam);
            return Err(crate::Error::MembershipSizeOfZero);
        } else if amalgam.pvalues.len() == 0 {
            error!("Found the pvalues len of zero for amalgam: {:?}", amalgam);
            return Err(crate::Error::MembershipSizeOfZero);
        }
        let mut pvalues = amalgam.pvalues;
        let wgm = aggregate_pvalues(&mut pvalues, amalgam.weight_config);
        let logfc = arithmetic_mean(&amalgam.logfc);
        let gene = format!("amalgam_{}_{}", amalgam.membership_size, amalgam.draw_index);
        Ok(GeneResult::builder()
            .gene(gene)
            .wgm(wgm)
            .logfc(logfc)
            .amalgam(true)
            .build())
    }
}