optimized lres collapse (0e8980ae) · Commits · github_fork / Presto 20250701

R/glmm.R

+38 −9

Original line number	Diff line number	Diff line
		@@ -188,6 +188,32 @@ make_betanames_df <- function(model, has_offset) {

		}

		#' @export
		collapse_lres <- function(lres) {
		res <- list()
		res$beta <- purrr::map(lres, 'beta') %>% collapse_vecs(length(lres))
		colnames(res$beta) <- names(lres)

		res$epsilon <- purrr::map(lres, 'epsilon') %>% collapse_vecs(length(lres))
		colnames(res$epsilon) <- names(lres)

		res$epsilon_pearson <- purrr::map(lres, 'epsilon_pearson') %>% collapse_vecs(length(lres))
		colnames(res$epsilon_pearson) <- names(lres)

		res$prior_sd <- purrr::map(lres, 'prior_sd') %>% collapse_vecs(length(lres))
		colnames(res$prior_sd) <- names(lres)

		covmat_list <- purrr::map(lres, 'covmat')
		res$covmat <- collapse_mats(covmat_list, length(covmat_list))
		dnames <- dimnames(covmat_list[[1]])
		dnames[[3]] <- names(covmat_list)
		dimnames(res$covmat) <- dnames

		return(res)
		}



		#' @export
		presto.presto <- function(
		formula,
		@@ -259,15 +285,17 @@ presto.presto <- function(
		if (verbose > 0) {
		message('Aggregate the results')
		}
		common_el <- purrr::reduce(map(lres, names), intersect) %>% setdiff('status')
		res <- map(common_el, function(name) {
		if (name == 'covmat') {
		purrr::reduce(purrr::map(lres, name), abind::abind, along = 3)
		} else {
		as.matrix(purrr::map_dfr(lres, name))
		}
		})
		names(res) <- common_el
		res <- collapse_lres(lres)

		# common_el <- purrr::reduce(map(lres, names), intersect) %>% setdiff('status')
		# res <- map(common_el, function(name) {
		# if (name == 'covmat') {
		# purrr::reduce(purrr::map(lres, name), abind::abind, along = 3)
		# } else {
		# as.matrix(purrr::map_dfr(lres, name))
		# }
		# })
		# names(res) <- common_el

		## clean up names in covmat
		if (verbose > 0) {
		@@ -323,6 +351,7 @@ presto.presto <- function(




		#' @export
		correct_counts <- function(object, effects_remove, umi_common, verbose=0) {

src/utils.cpp

0 → 100644

+37 −0

Original line number	Diff line number	Diff line
		#include <RcppArmadillo.h>
		#include <Rcpp.h>
		#include <iostream>
		#include <vector>
		#include <algorithm>
		using namespace Rcpp;

		// [[Rcpp::depends(RcppArmadillo)]]
		// [[Rcpp::depends(Rcpp]]


		using namespace std;


		// [[Rcpp::export]]
		arma::cube collapse_mats(vector<arma::mat> mat_list, unsigned n) {
		// arma::cube result = arma::zeros<arma::cube>(10, 10, n);
		arma::cube result = arma::zeros<arma::cube>(mat_list[0].n_rows, mat_list[0].n_cols, n);
		for (int i = 0; i < n; i++) {
		result.slice(i) = mat_list[i];
		}
		return result;
		}


		// [[Rcpp::export]]
		arma::mat collapse_vecs(vector<arma::vec> vec_list, unsigned n) {
		// arma::cube result = arma::zeros<arma::cube>(10, 10, n);
		arma::mat result = arma::zeros<arma::mat>(vec_list[0].n_elem, n);
		for (int i = 0; i < n; i++) {
		result.col(i) = vec_list[i];
		}
		return result;
		}

vignettes/pseudobulk.ipynb

+603 −780

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